7VSO | pdb_00007vso

Serial Femtosecond Crystallography (SFX) of Ground State Bacteriorhodopsin Crystallized from Bicelles in Complex with HAD16 Determined Using 7-keV X-ray Free Electron Laser (XFEL) at SACLA

PDB DOI: https://doi.org/10.2210/pdb7VSO/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Halobacterium salinarum
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD mpstruc

Deposited: 2021-10-27 Released: 2022-02-16
Deposition Author(s): Mizohata, E., Nakane, T., Hanashima, S.
Funding Organization(s): Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.35 Å
R-Value Free:
0.210 (Depositor), 0.210 (DCC)
R-Value Work:
0.158 (Depositor), 0.158 (DCC)
R-Value Observed:
0.160 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Heavy Atom Detergent/Lipid Combined X-ray Crystallography for Elucidating the Structure-Function Relationships of Membrane Proteins.

Hanashima, S., Nakane, T., Mizohata, E.

(2021) Membranes (Basel) 11

PubMed: 34832053 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.3390/membranes11110823
Primary Citation Related Structures:
7VSO

PubMed Abstract:
Membrane proteins reside in the lipid bilayer of biomembranes and the structure and function of these proteins are closely related to their interactions with lipid molecules. Structural analyses of interactions between membrane proteins and lipids or detergents that constitute biological or artificial model membranes are important for understanding the functions and physicochemical properties of membrane proteins and biomembranes. Determination of membrane protein structures is much more difficult when compared with that of soluble proteins, but the development of various new technologies has accelerated the elucidation of the structure-function relationship of membrane proteins. This review summarizes the development of heavy atom derivative detergents and lipids that can be used for structural analysis of membrane proteins and their interactions with detergents/lipids, including their application with X-ray free-electron laser crystallography.

Organizational Affiliation

Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka 563-0043, Japan.

Macromolecule Content

Total Structure Weight: 31.07 kDa
Atom Count: 2,067
Modeled Residue Count: 224
Deposited Residue Count: 249
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bacteriorhodopsin	A	249	Halobacterium salinarum	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for P02945 (Halobacterium salinarum (strain ATCC 700922 / JCM 11081 / NRC-1)) Explore P02945 Go to UniProtKB: P02945
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02945
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7YH (Subject of Investigation/LOI) Query on 7YH Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-[[(2R)-2-(3-bromanyl-5-iodanyl-phenyl)carbonyloxy-3-tetradecanoyloxy-propoxy]-oxidanyl-phosphoryl]oxyethyl-trimethyl-azanium C₂₉ H₄₉ Br I N O₈ P RDKBFTQTYYTUKD-HHHXNRCGSA-O		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
CPS (Subject of Investigation/LOI) Query on CPS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	3-[(3-CHOLAMIDOPROPYL)DIMETHYLAMMONIO]-1-PROPANESULFONATE C₃₂ H₅₈ N₂ O₇ S UMCMPZBLKLEWAF-BCTGSCMUSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
R16 (Subject of Investigation/LOI) Query on R16 Download:Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth A] SDF format, chain S [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A] MOL2 format, chain S [auth A] mmCIF format, chain I [auth A] mmCIF format, chain K [auth A] mmCIF format, chain S [auth A]	I [auth A], K [auth A], S [auth A]	HEXADECANE C₁₆ H₃₄ DCAYPVUWAIABOU-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth A] Focus chain S [auth A] Interactions & Density Focus chain I [auth A] Focus chain K [auth A] Focus chain S [auth A]
D12 (Subject of Investigation/LOI) Query on D12 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] MOL2 format, chain H [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] mmCIF format, chain H [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A]	H [auth A], Q [auth A], R [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth A] Focus chain R [auth A] Interactions & Density Focus chain H [auth A] Focus chain Q [auth A] Focus chain R [auth A]
D10 (Subject of Investigation/LOI) Query on D10 Download:Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain J [auth A] MOL2 format, chain M [auth A] MOL2 format, chain J [auth A] mmCIF format, chain M [auth A] mmCIF format, chain J [auth A]	J [auth A], M [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain M [auth A] Interactions & Density Focus chain J [auth A] Focus chain M [auth A]
DD9 (Subject of Investigation/LOI) Query on DD9 Download:Ideal Coordinates CCD File SDF format, chain P [auth A] MOL2 format, chain P [auth A] mmCIF format, chain P [auth A]	P [auth A]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain P [auth A] Interactions & Density Focus chain P [auth A]
IOD (Subject of Investigation/LOI) Query on IOD Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
OCT (Subject of Investigation/LOI) Query on OCT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain U [auth A] MOL2 format, chain F [auth A] MOL2 format, chain U [auth A] mmCIF format, chain F [auth A] mmCIF format, chain U [auth A]	F [auth A], U [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain U [auth A] Interactions & Density Focus chain F [auth A] Focus chain U [auth A]
HP6 (Subject of Investigation/LOI) Query on HP6 Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain O [auth A] SDF format, chain T [auth A] MOL2 format, chain G [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain O [auth A] MOL2 format, chain T [auth A] mmCIF format, chain G [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain O [auth A] mmCIF format, chain T [auth A]	G [auth A], L [auth A], N [auth A], O [auth A], T [auth A]	HEPTANE C₇ H₁₆ IMNFDUFMRHMDMM-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth A] Interactions & Density Focus chain G [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain T [auth A]