6UH3 | pdb_00006uh3

Crystal structure of bacterial heliorhodopsin 48C12

PDB DOI: https://doi.org/10.2210/pdb6UH3/pdb

Classification: SIGNALING PROTEIN
Organism(s): Actinomycetes bacterium
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2019-09-26 Released: 2019-12-04
Deposition Author(s): Lu, Y., Zhou, X.E., Gao, X., Xia, R., Xu, Z., Wang, N., Leng, Y., Melcher, K., Xu, H.E., He, Y.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free:
0.279 (Depositor), 0.280 (DCC)
R-Value Work:
0.264 (Depositor), 0.265 (DCC)
R-Value Observed:
0.265 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal structure of heliorhodopsin 48C12.

Lu, Y., Zhou, X.E., Gao, X., Wang, N., Xia, R., Xu, Z., Leng, Y., Shi, Y., Wang, G., Melcher, K., Xu, H.E., He, Y.

(2020) Cell Res 30: 88-90

PubMed: 31879417 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41422-019-0266-0
Primary Citation Related Structures:
6UH3

Organizational Affiliation

Laboratory of Receptor Structure and Signaling, HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, Heilongjiang, 150001, China.

Macromolecule Content

Total Structure Weight: 60.27 kDa
Atom Count: 4,190
Modeled Residue Count: 491
Deposited Residue Count: 504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heliorhodopsin	A, B	252	Actinomycetes bacterium	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for A0A2R4S913 (uncultured Actinomycetes bacterium) Explore A0A2R4S913 Go to UniProtKB: A0A2R4S913
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A2R4S913
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RET (Subject of Investigation/LOI) Query on RET Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain Q [auth B] MOL2 format, chain C [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain C [auth A] mmCIF format, chain Q [auth B]	C [auth A], Q [auth B]	RETINAL C₂₀ H₂₈ O NCYCYZXNIZJOKI-OVSJKPMPSA-N		Interactions Focus chain C [auth A] Focus chain Q [auth B] Interactions & Density Focus chain C [auth A] Focus chain Q [auth B]
PLM Query on PLM Download:Ideal Coordinates CCD File SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain O [auth A] SDF format, chain P [auth A] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain O [auth A] MOL2 format, chain P [auth A] mmCIF format, chain DA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain O [auth A] mmCIF format, chain P [auth A]	DA [auth B], EA [auth B], O [auth A], P [auth A]	PALMITIC ACID C₁₆ H₃₂ O₂ IPCSVZSSVZVIGE-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain EA [auth B] Focus chain O [auth A] Focus chain P [auth A] Interactions & Density Focus chain DA [auth B] Focus chain EA [auth B] Focus chain O [auth A] Focus chain P [auth A]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain AA [auth B] SDF format, chain BA [auth B] SDF format, chain CA [auth B] SDF format, chain D [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain S [auth B] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain X [auth B] SDF format, chain R [auth B] SDF format, chain N [auth A] SDF format, chain M [auth A] SDF format, chain E [auth A] MOL2 format, chain AA [auth B] MOL2 format, chain BA [auth B] MOL2 format, chain CA [auth B] MOL2 format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain S [auth B] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain X [auth B] MOL2 format, chain R [auth B] MOL2 format, chain N [auth A] MOL2 format, chain M [auth A] MOL2 format, chain E [auth A] mmCIF format, chain AA [auth B] mmCIF format, chain BA [auth B] mmCIF format, chain CA [auth B] mmCIF format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain S [auth B] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain X [auth B] mmCIF format, chain R [auth B] mmCIF format, chain N [auth A] mmCIF format, chain M [auth A] mmCIF format, chain E [auth A]	AA [auth B] BA [auth B] CA [auth B] D [auth A] E [auth A] AA [auth B], BA [auth B], CA [auth B], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], R [auth B], S [auth B], U [auth B], V [auth B], X [auth B], Y [auth B], Z [auth B]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain BA [auth B] Focus chain CA [auth B] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain N [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain U [auth B] Focus chain V [auth B] Focus chain X [auth B] Focus chain Y [auth B] Focus chain Z [auth B]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain T [auth B] SDF format, chain W [auth B] MOL2 format, chain T [auth B] MOL2 format, chain W [auth B] mmCIF format, chain T [auth B] mmCIF format, chain W [auth B]	T [auth B], W [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain T [auth B] Focus chain W [auth B] Interactions & Density Focus chain T [auth B] Focus chain W [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.279 (Depositor), 0.280 (DCC)
R-Value Work: 0.264 (Depositor), 0.265 (DCC)
R-Value Observed: 0.265 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.449	α = 90
b = 102.139	β = 94.04
c = 56.77	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-12-04

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2019-12-04
Type: Initial release
Version 1.1: 2019-12-11
Changes: Database references, Structure summary
Version 1.2: 2020-01-08
Changes: Database references
Version 1.3: 2020-01-22
Changes: Database references
Version 1.4: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.5: 2024-11-20
Changes: Structure summary