6CMO

Rhodopsin-Gi complex

• PDB DOI: https://doi.org/10.2210/pdb6CMO/pdb
• EM Map EMD-7517: EMDB EMDataResource

• Classification: SIGNALING PROTEIN
• Organism(s): Escherichia coli, Homo sapiens, Rattus norvegicus, Bos taurus, synthetic construct
• Expression System: Spodoptera frugiperda, Bacteria Latreille et al. 1825
• Mutation(s): No 
• Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc


• Deposited: 2018-03-05 Released: 2018-06-20 
• Deposition Author(s): Kang, Y., Kuybeda, O., de Waal, P.W., Mukherjee, S., Van Eps, N., Dutka, P., Zhou, X.E., Bartesaghi, A., Erramilli, S., Morizumi, T., Gu, X., Yin, Y., Liu, P., Jiang, Y., Meng, X., Zhao, G., Melcher, K., Earnst, O.P., Kossiakoff, A.A., Subramaniam, S., Xu, H.E.
• Funding Organization(s): National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK), American Asthma Foundation, Jay and Betty Van Andel Foundation, Ministry of Science and Technology (MoST, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A1B1C1D1E1F1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer - A2B1C1D1E1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: cross-linking

Macromolecule Content

• Total Structure Weight: 187.78 kDa 
• Atom Count: 11,834 
• Modelled Residue Count: 1,516 
• Deposited Residue Count: 1,684 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
chimera protein of Soluble cytochrome b562 and Rhodopsin	A [auth R]	463	Escherichia coli, Homo sapiens This entity is chimeric	Mutation(s): 0  Gene Names: cybC, RHO, OPN2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P0ABE7 (Escherichia coli) Explore P0ABE7  Go to UniProtKB:  P0ABE7
Find proteins for P08100 (Homo sapiens) Explore P08100  Go to UniProtKB:  P08100
PHAROS:  P08100 GTEx:  ENSG00000163914
UniProt Groups	P0ABE7P08100

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	B [auth A]	354	Homo sapiens	Mutation(s): 0  Gene Names: GNAI1 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P63096 (Homo sapiens) Explore P63096  Go to UniProtKB:  P63096
PHAROS:  P63096 GTEx:  ENSG00000127955

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	C [auth B]	345	Rattus norvegicus	Mutation(s): 0  Gene Names: Gnb1
UniProt
Find proteins for P54311 (Rattus norvegicus) Explore P54311  Go to UniProtKB:  P54311

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	D [auth G]	68	Bos taurus	Mutation(s): 0  Gene Names: GNG2 Membrane Entity: Yes
UniProt
Find proteins for P63212 (Bos taurus) Explore P63212  Go to UniProtKB:  P63212

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab light chain	E [auth L]	215	synthetic construct	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab Heavy chain	F [auth H]	239	synthetic construct	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 7
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G [auth C]	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-06-20 
Deposition Author(s): Kang, Y., Kuybeda, O., de Waal, P.W., Mukherjee, S., Van Eps, N., Dutka, P., Zhou, X.E., Bartesaghi, A., Erramilli, S., Morizumi, T., Gu, X., Yin, Y., Liu, P., Jiang, Y., Meng, X., Zhao, G., Melcher, K., Earnst, O.P., Kossiakoff, A.A., Subramaniam, S., Xu, H.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)	United States	DK071662
American Asthma Foundation	United States	--
Jay and Betty Van Andel Foundation	United States	--
Ministry of Science and Technology (MoST, China)	China	2012ZX09301001 and 2012CB910403, 2013CB910600, XDB08020303, 2013ZX09507001

Revision History  

• Version 1.0: 2018-06-20
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Source and taxonomy
• Version 1.2: 2018-10-24
  Changes: Data collection, Database references, Structure summary
• Version 1.3: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2019-04-17
  Changes: Author supporting evidence, Data collection
• Version 1.5: 2019-12-18
  Changes: Author supporting evidence, Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary