8B5L

Cryo-EM structure of ribosome-Sec61-TRAP (TRanslocon Associated Protein) translocon complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into TRAP association with ribosome-Sec61 complex and translocon inhibition by a CADA derivative.

Pauwels, E.Shewakramani, N.R.De Wijngaert, B.Camps, A.Provinciael, B.Stroobants, J.Kalies, K.U.Hartmann, E.Maes, P.Vermeire, K.Das, K.

(2023) Sci Adv 9: eadf0797-eadf0797

  • DOI: https://doi.org/10.1126/sciadv.adf0797
  • Primary Citation of Related Structures:  
    8B5L, 8B6C

  • PubMed Abstract: 

    During cotranslational translocation, the signal peptide of a nascent chain binds Sec61 translocon to initiate protein transport through the endoplasmic reticulum (ER) membrane. Our cryo-electron microscopy structure of ribosome-Sec61 shows binding of an ordered heterotetrameric translocon-associated protein (TRAP) complex, in which TRAP-γ is anchored at two adjacent positions of 28 S ribosomal RNA and interacts with ribosomal protein L38 and Sec61α/γ. Four transmembrane helices (TMHs) of TRAP-γ cluster with one C-terminal helix of each α, β, and δ subunits. The seven TMH bundle helps position a crescent-shaped trimeric TRAP-α/β/δ core in the ER lumen, facing the Sec61 channel. Further, our in vitro assay establishes the cyclotriazadisulfonamide derivative CK147 as a translocon inhibitor. A structure of ribosome-Sec61-CK147 reveals CK147 binding the channel and interacting with the plug helix from the lumenal side. The CK147 resistance mutations surround the inhibitor. These structures help in understanding the TRAP functions and provide a new Sec61 site for designing translocon inhibitors.


  • Organizational Affiliation

    Department of Microbiology, Immunology, and Transplantation, KU Leuven, Leuven 3000, Belgium.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35A [auth h]122Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L17B [auth P]153Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SCJ6 (Oryctolagus cuniculus)
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L31C [auth d]107Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7aE [auth G]319Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L32F [auth e]128Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUN8 (Oryctolagus cuniculus)
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Signal sequence receptor subunit 3G [auth t]185Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A5F9DJN2 (Oryctolagus cuniculus)
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L18aH [auth S]176Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTY7 (Oryctolagus cuniculus)
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L10214Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L18_c domain-containing proteinJ [auth D]293Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P19949 (Oryctolagus cuniculus)
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L23K [auth V]131Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1T6D1 (Oryctolagus cuniculus)
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L6L [auth E]291Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SKF7 (Oryctolagus cuniculus)
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L11M [auth J]170Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TUB8 (Oryctolagus cuniculus)
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit alphaN [auth q]286Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TU86 (Oryctolagus cuniculus)
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L38O [auth k]70Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1U001 (Oryctolagus cuniculus)
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L29P [auth b]245Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SGR6 (Oryctolagus cuniculus)
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40Q [auth m]52Oryctolagus cuniculusMutation(s): 0 
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Find proteins for P0DXC2 (Oryctolagus cuniculus)
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27R [auth Z]135Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TXF6 (Oryctolagus cuniculus)
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L21S [auth T]159Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SHQ2 (Oryctolagus cuniculus)
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Entity ID: 20
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36T [auth i]105Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 21
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L7U [auth F]225Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SV32 (Oryctolagus cuniculus)
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Entity ID: 22
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L41V [auth n]25Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for A0A087WNH4 (Oryctolagus cuniculus)
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Entity ID: 23
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13W [auth L]211Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TKB3 (Oryctolagus cuniculus)
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Entity ID: 24
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L13aX [auth O]203Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TVS8 (Oryctolagus cuniculus)
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Entity ID: 26
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L4Z [auth C]362Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SVW5 (Oryctolagus cuniculus)
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Entity ID: 27
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L26AA [auth Y]134Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 28
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L3BA [auth B]394Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 29
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L19CA [auth R]196Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TYL6 (Oryctolagus cuniculus)
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Entity ID: 30
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal_L23eN domain-containing proteinDA [auth X]118Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1SE76 (Oryctolagus cuniculus)
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Entity ID: 31
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L37aEA [auth p]91Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 32
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L14FA [auth M]138Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 33
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L9GA [auth H]190Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 35
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L28IA [auth r]124Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 36
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L18JA [auth Q]188Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 37
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L35aKA [auth f]109Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 38
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L27aLA [auth a]147Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 39
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L8MA [auth A]257Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 40
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L34NA [auth g]114Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 41
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit deltaOA [auth K]173Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 42
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit gammaPA [auth u]68Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 43
MoleculeChains Sequence LengthOrganismDetailsImage
Translocon-associated protein subunit betaQA [auth v]183Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SV74 (Oryctolagus cuniculus)
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Entity ID: 44
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L37RA [auth j]86Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 45
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L15SA [auth N]203Oryctolagus cuniculusMutation(s): 0 
UniProt
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Entity ID: 46
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L36a-likeTA [auth o]103Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1T040 (Oryctolagus cuniculus)
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Entity ID: 47
MoleculeChains Sequence LengthOrganismDetailsImage
Protein transport protein Sec61 subunit alpha isoform 1UA [auth s]476Oryctolagus cuniculusMutation(s): 0 
UniProt
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UniProt GroupA0A5F9CHB7
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Entity ID: 48
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L30VA [auth c]98Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1TDL2 (Oryctolagus cuniculus)
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Entity ID: 49
MoleculeChains Sequence LengthOrganismDetailsImage
Ribosomal protein L24WA [auth W]157Oryctolagus cuniculusMutation(s): 0 
UniProt
Find proteins for G1SE28 (Oryctolagus cuniculus)
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Entity ID: 50
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L39-likeXA [auth l]50Oryctolagus cuniculusMutation(s): 0 
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Find proteins for G1TTN1 (Oryctolagus cuniculus)
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Entity ID: 51
MoleculeChains Sequence LengthOrganismDetailsImage
60S ribosomal protein L22YA [auth U]99Oryctolagus cuniculusMutation(s): 0 
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Entity ID: 4
MoleculeChains LengthOrganismImage
28S rRNAD [auth 5]4,808Oryctolagus cuniculus
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Entity ID: 25
MoleculeChains LengthOrganismImage
5.8S rRNAY [auth 8]156Oryctolagus cuniculus
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Entity ID: 34
MoleculeChains LengthOrganismImage
5S rRNAHA [auth 7]120Oryctolagus cuniculus
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Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
HH [auth m],
NH [auth p],
XH [auth g],
YH [auth j],
ZH [auth o]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
AB [auth 5]
AC [auth 5]
AD [auth 5]
AE [auth 5]
AF [auth 5]
AB [auth 5],
AC [auth 5],
AD [auth 5],
AE [auth 5],
AF [auth 5],
AG [auth 5],
AH [auth 5],
BB [auth 5],
BC [auth 5],
BD [auth 5],
BE [auth 5],
BF [auth 5],
BG [auth 5],
BH [auth 5],
CB [auth 5],
CC [auth 5],
CD [auth 5],
CE [auth 5],
CF [auth 5],
CG [auth 5],
CH [auth 5],
DB [auth 5],
DC [auth 5],
DD [auth 5],
DE [auth 5],
DF [auth 5],
DG [auth 5],
DH [auth 5],
EB [auth 5],
EC [auth 5],
ED [auth 5],
EE [auth 5],
EF [auth 5],
EG [auth 5],
EH [auth 5],
FB [auth 5],
FC [auth 5],
FD [auth 5],
FE [auth 5],
FF [auth 5],
FG [auth 5],
FH [auth I],
GB [auth 5],
GC [auth 5],
GD [auth 5],
GE [auth 5],
GF [auth 5],
GG [auth 5],
GH [auth V],
HB [auth 5],
HC [auth 5],
HD [auth 5],
HE [auth 5],
HF [auth 5],
HG [auth 5],
IB [auth 5],
IC [auth 5],
ID [auth 5],
IE [auth 5],
IF [auth 5],
IG [auth 5],
IH [auth 8],
JB [auth 5],
JC [auth 5],
JD [auth 5],
JE [auth 5],
JF [auth 5],
JG [auth 5],
JH [auth 8],
KB [auth 5],
KC [auth 5],
KD [auth 5],
KE [auth 5],
KF [auth 5],
KG [auth 5],
KH [auth 8],
LB [auth 5],
LC [auth 5],
LD [auth 5],
LE [auth 5],
LF [auth 5],
LG [auth 5],
LH [auth 8],
MB [auth 5],
MC [auth 5],
MD [auth 5],
ME [auth 5],
MF [auth 5],
MG [auth 5],
MH [auth 8],
NB [auth 5],
NC [auth 5],
ND [auth 5],
NE [auth 5],
NF [auth 5],
NG [auth 5],
OB [auth 5],
OC [auth 5],
OD [auth 5],
OE [auth 5],
OF [auth 5],
OG [auth 5],
OH [auth 7],
PB [auth 5],
PC [auth 5],
PD [auth 5],
PE [auth 5],
PF [auth 5],
PG [auth 5],
PH [auth 7],
QB [auth 5],
QC [auth 5],
QD [auth 5],
QE [auth 5],
QF [auth 5],
QG [auth 5],
QH [auth 7],
RB [auth 5],
RC [auth 5],
RD [auth 5],
RE [auth 5],
RF [auth 5],
RG [auth 5],
RH [auth 7],
SB [auth 5],
SC [auth 5],
SD [auth 5],
SE [auth 5],
SF [auth 5],
SG [auth 5],
SH [auth 7],
TB [auth 5],
TC [auth 5],
TD [auth 5],
TE [auth 5],
TF [auth 5],
TG [auth 5],
TH [auth 7],
UB [auth 5],
UC [auth 5],
UD [auth 5],
UE [auth 5],
UF [auth 5],
UG [auth 5],
UH [auth 7],
VB [auth 5],
VC [auth 5],
VD [auth 5],
VE [auth 5],
VF [auth 5],
VG [auth 5],
VH [auth a],
WB [auth 5],
WC [auth 5],
WD [auth 5],
WE [auth 5],
WF [auth 5],
WG [auth 5],
WH [auth A],
XB [auth 5],
XC [auth 5],
XD [auth 5],
XE [auth 5],
XF [auth 5],
XG [auth 5],
YB [auth 5],
YC [auth 5],
YD [auth 5],
YE [auth 5],
YF [auth 5],
YG [auth 5],
ZA [auth P],
ZB [auth 5],
ZC [auth 5],
ZD [auth 5],
ZE [auth 5],
ZF [auth 5],
ZG [auth 5]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
Q [auth m]L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.86 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION3.1
MODEL REFINEMENTPHENIX1.20

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
KU LeuvenBelgium--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-01
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references