6BAQ

Mus musculus BPIFA1

PDB DOI: https://doi.org/10.2210/pdb6BAQ/pdb

Classification: ANTIMICROBIAL PROTEIN
Organism(s): Mus musculus
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No
Membrane Protein: Yes OPM

Deposited: 2017-10-15 Released: 2018-05-09
Deposition Author(s): Little, M.S., Redinbo, M.R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278
R-Value Work: 0.221
R-Value Observed: 0.223

wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

Crystal structure of the mouse innate immunity factor bacterial permeability-increasing family member A1.

Little, M.S., Redinbo, M.R.

(2018) Acta Crystallogr F Struct Biol Commun 74: 268-276

PubMed: 29717993 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1107/S2053230X18004600
Primary Citation of Related Structures:
6BAQ

PubMed Abstract:
Bacterial permeability-increasing family member A1 (BPIFA1) is an innate immunity factor and one of the most abundantly secreted proteins in the upper airways. BPIFA1 is multifunctional, with antimicrobial, surfactant and lipopolysaccharide-binding activities, as well as established roles in lung hydration. Here, the 2.5 Å resolution crystal structure of BPIFA1 from Mus musculus (mBPIFA1) is presented and compared with those of human BPIFA1 (hBPIFA1) and structural homologs. Structural distinctions between mBPIFA1 and hBPIFA1 suggest potential differences in biological function, including the regulation of a key pulmonary ion channel.

Organizational Affiliation

Department of Chemistry, University of North Carolina, 4350 Genome Sciences Building, Chapel Hill, NC 27599-3290, USA.

Macromolecule Content

Total Structure Weight: 203.64 kDa
Atom Count: 11,470
Modelled Residue Count: 1,558
Deposited Residue Count: 1,952
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BPI fold-containing family A member 1	A, B, C, D, E A, B, C, D, E, F, G, H	244	Mus musculus	Mutation(s): 0 Gene Names: Bpifa1, Plunc, Splunc1 Membrane Entity: Yes
UniProt
Find proteins for P97361 (Mus musculus) Explore P97361 Go to UniProtKB: P97361
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P97361
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain AA [auth C] SDF format, chain BB [auth G] SDF format, chain PB [auth H] SDF format, chain QB [auth H] MOL2 format, chain AA [auth C] MOL2 format, chain BB [auth G] MOL2 format, chain PB [auth H] MOL2 format, chain QB [auth H]	AA [auth C], BB [auth G], PB [auth H], QB [auth H]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain AA [auth C] Focus chain BB [auth G] Focus chain PB [auth H] Focus chain QB [auth H] Interactions & Density Focus chain AA [auth C] Focus chain BB [auth G] Focus chain PB [auth H] Focus chain QB [auth H]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain Z [auth B] MOL2 format, chain Z [auth B]	Z [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain Z [auth B] Interactions & Density Focus chain Z [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain AB [auth F] SDF format, chain BA [auth C] SDF format, chain CA [auth C] SDF format, chain CB [auth G] SDF format, chain DA [auth C] SDF format, chain DB [auth G] SDF format, chain EA [auth C] SDF format, chain EB [auth G] SDF format, chain FA [auth C] SDF format, chain FB [auth G] SDF format, chain GA [auth C] SDF format, chain GB [auth G] SDF format, chain HA [auth C] SDF format, chain HB [auth G] SDF format, chain I [auth A] SDF format, chain IA [auth C] SDF format, chain IB [auth G] SDF format, chain J [auth A] SDF format, chain JA [auth D] SDF format, chain JB [auth G] SDF format, chain K [auth A] SDF format, chain KA [auth D] SDF format, chain KB [auth G] SDF format, chain L [auth A] SDF format, chain LA [auth D] SDF format, chain LB [auth G] SDF format, chain M [auth A] SDF format, chain MA [auth D] SDF format, chain MB [auth G] SDF format, chain N [auth A] SDF format, chain NA [auth E] SDF format, chain NB [auth G] SDF format, chain O [auth A] SDF format, chain OA [auth E] SDF format, chain OB [auth G] SDF format, chain P [auth A] SDF format, chain PA [auth E] SDF format, chain Q [auth A] SDF format, chain QA [auth E] SDF format, chain R [auth A] SDF format, chain RA [auth E] SDF format, chain RB [auth H] SDF format, chain S [auth A] SDF format, chain SA [auth E] SDF format, chain SB [auth H] SDF format, chain T [auth B] SDF format, chain TA [auth E] SDF format, chain TB [auth H] SDF format, chain U [auth B] SDF format, chain UA [auth E] SDF format, chain UB [auth H] SDF format, chain V [auth B] SDF format, chain VA [auth E] SDF format, chain VB [auth H] SDF format, chain W [auth B] SDF format, chain WA [auth F] SDF format, chain WB [auth H] SDF format, chain X [auth B] SDF format, chain XA [auth F] SDF format, chain XB [auth H] SDF format, chain Y [auth B] SDF format, chain YA [auth F] SDF format, chain ZA [auth F] MOL2 format, chain AB [auth F] MOL2 format, chain BA [auth C] MOL2 format, chain CA [auth C] MOL2 format, chain CB [auth G] MOL2 format, chain DA [auth C] MOL2 format, chain DB [auth G] MOL2 format, chain EA [auth C] MOL2 format, chain EB [auth G] MOL2 format, chain FA [auth C] MOL2 format, chain FB [auth G] MOL2 format, chain GA [auth C] MOL2 format, chain GB [auth G] MOL2 format, chain HA [auth C] MOL2 format, chain HB [auth G] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain IB [auth G] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth D] MOL2 format, chain JB [auth G] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth D] MOL2 format, chain KB [auth G] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth D] MOL2 format, chain LB [auth G] MOL2 format, chain M [auth A] MOL2 format, chain MA [auth D] MOL2 format, chain MB [auth G] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth E] MOL2 format, chain NB [auth G] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth E] MOL2 format, chain OB [auth G] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth E] MOL2 format, chain RB [auth H] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth E] MOL2 format, chain SB [auth H] MOL2 format, chain T [auth B] MOL2 format, chain TA [auth E] MOL2 format, chain TB [auth H] MOL2 format, chain U [auth B] MOL2 format, chain UA [auth E] MOL2 format, chain UB [auth H] MOL2 format, chain V [auth B] MOL2 format, chain VA [auth E] MOL2 format, chain VB [auth H] MOL2 format, chain W [auth B] MOL2 format, chain WA [auth F] MOL2 format, chain WB [auth H] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth F] MOL2 format, chain XB [auth H] MOL2 format, chain Y [auth B] MOL2 format, chain YA [auth F] MOL2 format, chain ZA [auth F]	AB [auth F] BA [auth C] CA [auth C] CB [auth G] DA [auth C] AB [auth F], BA [auth C], CA [auth C], CB [auth G], DA [auth C], DB [auth G], EA [auth C], EB [auth G], FA [auth C], FB [auth G], GA [auth C], GB [auth G], HA [auth C], HB [auth G], I [auth A], IA [auth C], IB [auth G], J [auth A], JA [auth D], JB [auth G], K [auth A], KA [auth D], KB [auth G], L [auth A], LA [auth D], LB [auth G], M [auth A], MA [auth D], MB [auth G], N [auth A], NA [auth E], NB [auth G], O [auth A], OA [auth E], OB [auth G], P [auth A], PA [auth E], Q [auth A], QA [auth E], R [auth A], RA [auth E], RB [auth H], S [auth A], SA [auth E], SB [auth H], T [auth B], TA [auth E], TB [auth H], U [auth B], UA [auth E], UB [auth H], V [auth B], VA [auth E], VB [auth H], W [auth B], WA [auth F], WB [auth H], X [auth B], XA [auth F], XB [auth H], Y [auth B], YA [auth F], ZA [auth F]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth G] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth E] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain V [auth B] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain W [auth B] Focus chain WA [auth F] Focus chain WB [auth H] Focus chain X [auth B] Focus chain XA [auth F] Focus chain XB [auth H] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain ZA [auth F] Interactions & Density Focus chain AB [auth F] Focus chain BA [auth C] Focus chain CA [auth C] Focus chain CB [auth G] Focus chain DA [auth C] Focus chain DB [auth G] Focus chain EA [auth C] Focus chain EB [auth G] Focus chain FA [auth C] Focus chain FB [auth G] Focus chain GA [auth C] Focus chain GB [auth G] Focus chain HA [auth C] Focus chain HB [auth G] Focus chain I [auth A] Focus chain IA [auth C] Focus chain IB [auth G] Focus chain J [auth A] Focus chain JA [auth D] Focus chain JB [auth G] Focus chain K [auth A] Focus chain KA [auth D] Focus chain KB [auth G] Focus chain L [auth A] Focus chain LA [auth D] Focus chain LB [auth G] Focus chain M [auth A] Focus chain MA [auth D] Focus chain MB [auth G] Focus chain N [auth A] Focus chain NA [auth E] Focus chain NB [auth G] Focus chain O [auth A] Focus chain OA [auth E] Focus chain OB [auth G] Focus chain P [auth A] Focus chain PA [auth E] Focus chain Q [auth A] Focus chain QA [auth E] Focus chain R [auth A] Focus chain RA [auth E] Focus chain RB [auth H] Focus chain S [auth A] Focus chain SA [auth E] Focus chain SB [auth H] Focus chain T [auth B] Focus chain TA [auth E] Focus chain TB [auth H] Focus chain U [auth B] Focus chain UA [auth E] Focus chain UB [auth H] Focus chain V [auth B] Focus chain VA [auth E] Focus chain VB [auth H] Focus chain W [auth B] Focus chain WA [auth F] Focus chain WB [auth H] Focus chain X [auth B] Focus chain XA [auth F] Focus chain XB [auth H] Focus chain Y [auth B] Focus chain YA [auth F] Focus chain ZA [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278
R-Value Work: 0.221
R-Value Observed: 0.223
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 132.2	α = 90
b = 200.582	β = 126.15
c = 89.499	γ = 90

Software Package:

Software Name	Purpose
Coot	refinement
PHENIX	refinement
PHENIX	model building
HKL-2000	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2018-05-09

Deposition Author(s):

Little, M.S.

Redinbo, M.R.

Revision History (Full details and data files)

Version 1.0: 2018-05-09
Type: Initial release
Version 1.1: 2018-12-19
Changes: Data collection, Database references
Version 1.2: 2019-04-24
Changes: Author supporting evidence, Data collection
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Derived calculations, Refinement description