7RKM | pdb_00007rkm

Structure of CX3CL1-US28-Gi-scFv16 in C-state

PDB DOI: https://doi.org/10.2210/pdb7RKM/pdb
EM Map EMD-24500: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Homo sapiens, Mus musculus, Human betaherpesvirus 5
Expression System: Trichoplusia ni, Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD mpstruc

Deposited: 2021-07-22 Released: 2022-01-26
Deposition Author(s): Tsutsumi, N., Qu, Q., Jude, K.M., Skiniotis, G., Garcia, K.C.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), Howard Hughes Medical Institute (HHMI)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins

Tsutsumi, N., Maeda, S., Qu, Q., Voegele, M., Jude, K.M., Suomivuori, C.M., Panova, O., Waghray, D., Kato, H.E., Velasco, A., Dror, R.O., Skiniotis, G., Kobilka, B.K., Garcia, K.C.

(2022) Sci Adv 8: eabl5442

DOI: https://doi.org/10.1126/sciadv.abl5442

Macromolecule Content

Total Structure Weight: 165.23 kDa
Atom Count: 9,491
Modeled Residue Count: 1,201
Deposited Residue Count: 1,474
Unique protein chains: 6

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(i) subunit alpha-1	A	353	Homo sapiens	Mutation(s): 0 Gene Names: GNAI1 EC: 3.6.5 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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P63096
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1	B	345	Homo sapiens	Mutation(s): 0 Gene Names: GNB1
UniProt & NIH Common Fund Data Resources
Find proteins for P62873 (Homo sapiens) Explore P62873 Go to UniProtKB: P62873
PHAROS: P62873 GTEx: ENSG00000078369
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62873
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2	C	67	Homo sapiens	Mutation(s): 0 Gene Names: GNG2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P59768 (Homo sapiens) Explore P59768 Go to UniProtKB: P59768
PHAROS: P59768 GTEx: ENSG00000186469
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P59768
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Antibody fragment scFv16	D	256	Mus musculus	Mutation(s): 0

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| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fractalkine	E [auth L]	91	Homo sapiens	Mutation(s): 0 Gene Names: CX3CL1, FKN, NTT, SCYD1, A-152E5.2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P78423 (Homo sapiens) Explore P78423 Go to UniProtKB: P78423
PHAROS: P78423 GTEx: ENSG00000006210
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P78423
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
G-protein coupled receptor homolog US28	F [auth R]	362	Human betaherpesvirus 5	Mutation(s): 0 Gene Names: US28 Membrane Entity: Yes
UniProt
Find proteins for P69332 (Human cytomegalovirus (strain AD169)) Explore P69332 Go to UniProtKB: P69332
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P69332
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download:Ideal Coordinates CCD File SDF format, chain G [auth R] MOL2 format, chain G [auth R] mmCIF format, chain G [auth R]	G [auth R]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain G [auth R] Interactions & Density Focus chain G [auth R]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PCA Query on PCA	E [auth L]	L-PEPTIDE LINKING	C₅ H₇ N O₃		GLN

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.50 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX
RECONSTRUCTION	RELION	3.1

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI125320
Howard Hughes Medical Institute (HHMI)	United States	--