5VOB

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21

PDB DOI: https://doi.org/10.2210/pdb5VOB/pdb

Classification: Viral Protein/Immune System
Organism(s): Human herpesvirus 5 strain Merlin, Human herpesvirus 5 strain 5508, Human herpesvirus 5 strain AD169, Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2017-05-02 Released: 2017-07-05
Deposition Author(s): Malito, E., Chandramouli, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free: 0.237
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 236.1 kDa
Atom Count: 14,099
Modelled Residue Count: 1,753
Deposited Residue Count: 2,079
Unique protein chains: 7

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein H	A	725	Human herpesvirus 5 strain Merlin	Mutation(s): 0 Gene Names: gH, UL75
UniProt
Find proteins for Q6SW67 (Human cytomegalovirus (strain Merlin)) Explore Q6SW67 Go to UniProtKB: Q6SW67
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6SW67
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Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein L	B	278	Human herpesvirus 5 strain 5508	Mutation(s): 0 Gene Names: gL, UL115
UniProt
Find proteins for Q68674 (Human cytomegalovirus (strain 5508)) Explore Q68674 Go to UniProtKB: Q68674
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q68674
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein UL128	C	171	Human herpesvirus 5 strain AD169	Mutation(s): 0 Gene Names: UL128
UniProt
Find proteins for P16837 (Human cytomegalovirus (strain AD169)) Explore P16837 Go to UniProtKB: P16837
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P16837
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein UL130	D	252	Human herpesvirus 5 strain Merlin	Mutation(s): 0 Gene Names: UL130
UniProt
Find proteins for F5HCP3 (Human cytomegalovirus (strain Merlin)) Explore F5HCP3 Go to UniProtKB: F5HCP3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	F5HCP3
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Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein UL131A	E	129	Human herpesvirus 5 strain Merlin	Mutation(s): 0 Gene Names: UL131A
UniProt
Find proteins for F5HET4 (Human cytomegalovirus (strain Merlin)) Explore F5HET4 Go to UniProtKB: F5HET4
Entity Groups
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UniProt Group	F5HET4
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Reference Sequence

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Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 8I21 heavy chain	F [auth H]	289	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for S6B291 (Homo sapiens) Explore S6B291 Go to UniProtKB: S6B291
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Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	S6B291
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Reference Sequence

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Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
Fab 8I21 light chain	G [auth L]	235	Homo sapiens	Mutation(s): 0 Gene Names: IGKV3-15
UniProt
Find proteins for Q6GMX0 (Homo sapiens) Explore Q6GMX0 Go to UniProtKB: Q6GMX0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6GMX0
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Reference Sequence

Oligosaccharides

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Entity ID: 8
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	H [auth F]	3		N-Glycosylation	Interactions Focus chain H [auth F] Interactions & Density Focus chain H [auth F]
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth D] SDF format, chain R [auth D] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain Q [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth D] MOL2 format, chain R [auth D] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth D]	I [auth A] J [auth A] K [auth A] L [auth A] M [auth A] I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth B], P [auth D], Q [auth D], R [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions 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 O [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D] Interactions & Density 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 O [auth B] Focus chain P [auth D] Focus chain Q [auth D] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.02 Å
R-Value Free: 0.237
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.163	α = 90
b = 145.422	β = 90
c = 173.658	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XSCALE	data scaling
PHENIX	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-07-05

Deposition Author(s):

Malito, E.

Chandramouli, S.

Revision History (Full details and data files)

Version 1.0: 2017-07-05
Type: Initial release
Version 1.1: 2017-07-12
Changes: Database references
Version 1.2: 2017-08-16
Changes: Data collection
Version 1.3: 2017-08-23
Changes: Database references
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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Help and Resources

5VOB

Crystal structure of HCMV Pentamer in complex with neutralizing antibody 8I21

Entity ID: 1

UniProt

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Entity ID: 2

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Entity ID: 3

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Entity ID: 4

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Entity ID: 5

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Entity ID: 6

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Entity ID: 7

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Entity ID: 8

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)