6PFY

Membrane Protein Megahertz Crystallography at the European XFEL, Photosystem I at synchrotron to 2.9 A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Membrane protein megahertz crystallography at the European XFEL.

Gisriel, C.Coe, J.Letrun, R.Yefanov, O.M.Luna-Chavez, C.Stander, N.E.Lisova, S.Mariani, V.Kuhn, M.Aplin, S.Grant, T.D.Dorner, K.Sato, T.Echelmeier, A.Cruz Villarreal, J.Hunter, M.S.Wiedorn, M.O.Knoska, J.Mazalova, V.Roy-Chowdhury, S.Yang, J.H.Jones, A.Bean, R.Bielecki, J.Kim, Y.Mills, G.Weinhausen, B.Meza, J.D.Al-Qudami, N.Bajt, S.Brehm, G.Botha, S.Boukhelef, D.Brockhauser, S.Bruce, B.D.Coleman, M.A.Danilevski, C.Discianno, E.Dobson, Z.Fangohr, H.Martin-Garcia, J.M.Gevorkov, Y.Hauf, S.Hosseinizadeh, A.Januschek, F.Ketawala, G.K.Kupitz, C.Maia, L.Manetti, M.Messerschmidt, M.Michelat, T.Mondal, J.Ourmazd, A.Previtali, G.Sarrou, I.Schon, S.Schwander, P.Shelby, M.L.Silenzi, A.Sztuk-Dambietz, J.Szuba, J.Turcato, M.White, T.A.Wrona, K.Xu, C.Abdellatif, M.H.Zook, J.D.Spence, J.C.H.Chapman, H.N.Barty, A.Kirian, R.A.Frank, M.Ros, A.Schmidt, M.Fromme, R.Mancuso, A.P.Fromme, P.Zatsepin, N.A.

(2019) Nat Commun 10: 5021-5021

  • DOI: https://doi.org/10.1038/s41467-019-12955-3
  • Primary Citation of Related Structures:  
    6PFY, 6PGK

  • PubMed Abstract: 

    The world's first superconducting megahertz repetition rate hard X-ray free-electron laser (XFEL), the European XFEL, began operation in 2017, featuring a unique pulse train structure with 886 ns between pulses. With its rapid pulse rate, the European XFEL may alleviate some of the increasing demand for XFEL beamtime, particularly for membrane protein serial femtosecond crystallography (SFX), leveraging orders-of-magnitude faster data collection. Here, we report the first membrane protein megahertz SFX experiment, where we determined a 2.9 Å-resolution SFX structure of the large membrane protein complex, Photosystem I, a > 1 MDa complex containing 36 protein subunits and 381 cofactors. We address challenges to megahertz SFX for membrane protein complexes, including growth of large quantities of crystals and the large molecular and unit cell size that influence data collection and analysis. The results imply that megahertz crystallography could have an important impact on structure determination of large protein complexes with XFELs.


  • Organizational Affiliation

    Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287-5001, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A1
A, G, Y
755Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A405 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A405 
Go to UniProtKB:  P0A405
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A405
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I P700 chlorophyll a apoprotein A2
B, H, Z
741Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A407 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A407 
Go to UniProtKB:  P0A407
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A407
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I iron-sulfur centerAA [auth a],
C,
N
81Thermosynechococcus vestitus BP-1Mutation(s): 0 
EC: 1.97.1.12
Membrane Entity: Yes 
UniProt
Find proteins for P0A415 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A415 
Go to UniProtKB:  P0A415
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A415
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIBA [auth b],
D,
O
139Thermosynechococcus vestitus BP-1Mutation(s): 0 
UniProt
Find proteins for P0A420 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A420 
Go to UniProtKB:  P0A420
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A420
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IVCA [auth c],
E,
P
76Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A423 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A423 
Go to UniProtKB:  P0A423
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A423
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IIIDA [auth d],
F,
Q
164Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A401 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A401 
Go to UniProtKB:  P0A401
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A401
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit VIIIEA [auth e],
I,
R
38Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A427 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A427 
Go to UniProtKB:  P0A427
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A427
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit IXFA [auth f],
J,
S
41Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A429 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A429 
Go to UniProtKB:  P0A429
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A429
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit PsaKGA [auth g],
K,
T
83Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A425 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A425 
Go to UniProtKB:  P0A425
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A425
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIHA [auth h],
L,
U
155Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DGB4 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DGB4 
Go to UniProtKB:  Q8DGB4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DGB4
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I reaction center subunit XIIIA [auth i],
M,
V
31Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for P0A403 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore P0A403 
Go to UniProtKB:  P0A403
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A403
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
Photosystem I 4.8K proteinJA [auth j],
W,
X
39Thermosynechococcus vestitus BP-1Mutation(s): 0 
Membrane Entity: Yes 
UniProt
Find proteins for Q8DKP6 (Thermosynechococcus vestitus (strain NIES-2133 / IAM M-273 / BP-1))
Explore Q8DKP6 
Go to UniProtKB:  Q8DKP6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DKP6
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 8 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CLA (Subject of Investigation/LOI)
Query on CLA

Download Ideal Coordinates CCD File 
AB [auth A]
AC [auth A]
AD [auth B]
AF [auth G]
AG [auth G]
AB [auth A],
AC [auth A],
AD [auth B],
AF [auth G],
AG [auth G],
AH [auth H],
AI [auth H],
AJ [auth L],
AK [auth U],
AL [auth Y],
AN [auth Z],
AP [auth j],
BB [auth A],
BD [auth B],
BF [auth G],
BG [auth G],
BH [auth H],
BI [auth H],
BJ [auth L],
BK [auth U],
BL [auth Y],
BN [auth Z],
CB [auth A],
CD [auth B],
CF [auth G],
CG [auth G],
CH [auth H],
CI [auth H],
CJ [auth L],
CL [auth Y],
CN [auth Z],
DB [auth A],
DD [auth B],
DF [auth G],
DG [auth G],
DH [auth H],
DI [auth H],
DL [auth Y],
DN [auth Z],
EB [auth A],
ED [auth B],
EF [auth G],
EG [auth G],
EH [auth H],
EL [auth Y],
EN [auth Z],
FB [auth A],
FD [auth B],
FF [auth G],
FH [auth H],
FK [auth W],
FL [auth Y],
FN [auth Z],
GB [auth A],
GD [auth B],
GF [auth G],
GH [auth H],
GK [auth X],
GL [auth Y],
GN [auth Z],
HB [auth A],
HD [auth B],
HF [auth G],
HH [auth H],
HL [auth Y],
HN [auth Z],
IB [auth A],
ID [auth B],
IF [auth G],
IH [auth H],
IK [auth Y],
IL [auth Y],
IM [auth Z],
IN [auth Z],
IO [auth d],
JB [auth A],
JD [auth B],
JF [auth G],
JH [auth H],
JJ [auth Q],
JK [auth Y],
JL [auth Y],
JM [auth Z],
JN [auth Z],
JO [auth d],
KB [auth A],
KD [auth B],
KF [auth G],
KH [auth H],
KK [auth Y],
KL [auth Y],
KM [auth Z],
KN [auth Z],
LA [auth A],
LB [auth A],
LC [auth A],
LD [auth B],
LF [auth G],
LH [auth H],
LK [auth Y],
LL [auth Y],
LM [auth Z],
LN [auth Z],
MA [auth A],
MB [auth A],
MC [auth B],
MD [auth B],
MF [auth G],
MH [auth H],
MK [auth Y],
ML [auth Y],
MM [auth Z],
MN [auth Z],
MO [auth f],
NA [auth A],
NB [auth A],
NC [auth B],
ND [auth B],
NE [auth F],
NF [auth G],
NH [auth H],
NJ [auth S],
NK [auth Y],
NL [auth Y],
NM [auth Z],
NN [auth Z],
NO [auth f],
OA [auth A],
OB [auth A],
OC [auth B],
OD [auth B],
OF [auth G],
OG [auth G],
OH [auth H],
OI [auth H],
OJ [auth S],
OK [auth Y],
OL [auth Y],
OM [auth Z],
ON [auth Z],
PA [auth A],
PB [auth A],
PC [auth B],
PD [auth B],
PF [auth G],
PG [auth G],
PH [auth H],
PJ [auth S],
PK [auth Y],
PL [auth Y],
PM [auth Z],
PN [auth Z],
PO [auth g],
QA [auth A],
QB [auth A],
QC [auth B],
QD [auth B],
QE [auth G],
QF [auth G],
QG [auth H],
QH [auth H],
QK [auth Y],
QL [auth Y],
QM [auth Z],
QN [auth Z],
QO [auth g],
RA [auth A],
RB [auth A],
RC [auth B],
RD [auth B],
RE [auth G],
RF [auth G],
RG [auth H],
RH [auth H],
RI [auth J],
RK [auth Y],
RL [auth Y],
RM [auth Z],
RN [auth Z],
RO [auth h],
SA [auth A],
SB [auth A],
SC [auth B],
SD [auth B],
SE [auth G],
SF [auth G],
SG [auth H],
SH [auth H],
SI [auth J],
SJ [auth T],
SK [auth Y],
SL [auth Y],
SM [auth Z],
SN [auth Z],
TA [auth A],
TB [auth A],
TC [auth B],
TD [auth B],
TE [auth G],
TF [auth G],
TG [auth H],
TH [auth H],
TK [auth Y],
TL [auth Y],
TM [auth Z],
TN [auth Z],
UA [auth A],
UB [auth A],
UC [auth B],
UD [auth B],
UE [auth G],
UF [auth G],
UG [auth H],
UH [auth H],
UJ [auth T],
UK [auth Y],
UL [auth Y],
UM [auth Z],
UN [auth Z],
UO [auth h],
VA [auth A],
VB [auth A],
VC [auth B],
VD [auth B],
VE [auth G],
VF [auth G],
VG [auth H],
VH [auth H],
VI [auth K],
VK [auth Y],
VL [auth Y],
VM [auth Z],
VN [auth Z],
VO [auth h],
WA [auth A],
WB [auth A],
WC [auth B],
WD [auth B],
WE [auth G],
WF [auth G],
WG [auth H],
WH [auth H],
WI [auth K],
WJ [auth U],
WK [auth Y],
WM [auth Z],
WN [auth Z],
WO [auth h],
XA [auth A],
XB [auth A],
XC [auth B],
XD [auth B],
XE [auth G],
XF [auth G],
XG [auth H],
XH [auth H],
XI [auth L],
XJ [auth U],
XK [auth Y],
XM [auth Z],
YA [auth A],
YB [auth A],
YC [auth B],
YD [auth B],
YE [auth G],
YF [auth G],
YG [auth H],
YH [auth H],
YI [auth L],
YJ [auth U],
YK [auth Y],
YM [auth Z],
ZA [auth A],
ZB [auth A],
ZC [auth B],
ZD [auth B],
ZE [auth G],
ZF [auth G],
ZG [auth H],
ZH [auth H],
ZK [auth Y],
ZM [auth Z]
CHLOROPHYLL A
C55 H72 Mg N4 O5
ATNHDLDRLWWWCB-AENOIHSZSA-M
CL0 (Subject of Investigation/LOI)
Query on CL0

Download Ideal Coordinates CCD File 
HK [auth Y],
KA [auth A],
PE [auth G]
CHLOROPHYLL A ISOMER
C55 H72 Mg N4 O5
VIQFHHZSLDFWDU-DVXFRRMCSA-M
LMG (Subject of Investigation/LOI)
Query on LMG

Download Ideal Coordinates CCD File 
EO [auth Z],
HE [auth B],
LI [auth H]
1,2-DISTEAROYL-MONOGALACTOSYL-DIGLYCERIDE
C45 H86 O10
DCLTVZLYPPIIID-CVELTQQQSA-N
LHG (Subject of Investigation/LOI)
Query on LHG

Download Ideal Coordinates CCD File 
EM [auth Y]
FM [auth Y]
IE [auth B]
JC [auth A]
KC [auth A]
EM [auth Y],
FM [auth Y],
IE [auth B],
JC [auth A],
KC [auth A],
MG [auth G],
MI [auth H],
NG [auth G],
ZO [auth j]
1,2-DIPALMITOYL-PHOSPHATIDYL-GLYCEROLE
C38 H75 O10 P
BIABMEZBCHDPBV-MPQUPPDSSA-N
BCR (Subject of Investigation/LOI)
Query on BCR

Download Ideal Coordinates CCD File 
AM [auth Y]
AO [auth Z]
BE [auth B]
BM [auth Y]
BO [auth Z]
AM [auth Y],
AO [auth Z],
BE [auth B],
BM [auth Y],
BO [auth Z],
CE [auth B],
CK [auth U],
CM [auth Y],
CO [auth Z],
DC [auth A],
DE [auth B],
DJ [auth L],
DK [auth U],
DM [auth Y],
DO [auth Z],
EC [auth A],
EE [auth B],
EJ [auth L],
EK [auth V],
FC [auth A],
FE [auth B],
FI [auth H],
FJ [auth M],
FO [auth Z],
GC [auth A],
GE [auth B],
GI [auth H],
GM [auth Y],
HC [auth A],
HG [auth G],
HI [auth H],
HM [auth Y],
IC [auth A],
IG [auth G],
II [auth H],
IJ [auth Q],
JE [auth B],
JG [auth G],
JI [auth H],
KG [auth G],
KI [auth H],
KJ [auth Q],
KO [auth d],
LG [auth G],
LJ [auth R],
LO [auth e],
ME [auth F],
MJ [auth R],
NI [auth H],
OE [auth F],
OO [auth f],
PI [auth I],
QI [auth I],
QJ [auth S],
RJ [auth S],
SO [auth h],
TI [auth J],
TJ [auth T],
UI [auth J],
XO [auth h],
YL [auth Y],
YN [auth Z],
YO [auth i],
ZJ [auth U],
ZL [auth Y],
ZN [auth Z]
BETA-CAROTENE
C40 H56
OENHQHLEOONYIE-JLTXGRSLSA-N
PQN (Subject of Investigation/LOI)
Query on PQN

Download Ideal Coordinates CCD File 
AE [auth B]
BC [auth A]
EI [auth H]
FG [auth G]
WL [auth Y]
AE [auth B],
BC [auth A],
EI [auth H],
FG [auth G],
WL [auth Y],
XN [auth Z]
PHYLLOQUINONE
C31 H46 O2
MBWXNTAXLNYFJB-NKFFZRIASA-N
SF4 (Subject of Investigation/LOI)
Query on SF4

Download Ideal Coordinates CCD File 
CC [auth A]
GG [auth G]
GJ [auth N]
GO [auth a]
HJ [auth N]
CC [auth A],
GG [auth G],
GJ [auth N],
GO [auth a],
HJ [auth N],
HO [auth a],
KE [auth C],
LE [auth C],
XL [auth Y]
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)
Query on CA

Download Ideal Coordinates CCD File 
TO [auth h],
VJ [auth U],
ZI [auth L]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.343 
  • R-Value Work: 0.303 
  • R-Value Observed: 0.305 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 278.496α = 90
b = 165.126β = 119.42
c = 283.427γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Released Date: 2019-11-20 
  • Deposition Author(s): Fromme, R.

Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-20
    Type: Initial release
  • Version 1.1: 2019-12-04
    Changes: Author supporting evidence
  • Version 2.0: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Non-polymer description, Refinement description