5ZS0 | pdb_00005zs0

Structure of glycoprotein B Domain IV of pseudorabies virus with 7B11 antibody

PDB DOI: https://doi.org/10.2210/pdb5ZS0/pdb

Classification: VIRAL PROTEIN
Organism(s): Mus musculus, Suid alphaherpesvirus 1
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2018-04-26 Released: 2019-05-22
Deposition Author(s): Hu, X.L., Yang, F.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free:
0.310 (Depositor), 0.313 (DCC)
R-Value Work:
0.241 (Depositor), 0.249 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Structural Basis for the Recognition of Pseudorabies Virus Glycoprotein B by a Complement-dependent Neutralizing Antibody

Hu, X.L., Peng, R.C., Li, X.D.

To be published.

Macromolecule Content

Total Structure Weight: 74.42 kDa
Atom Count: 4,628
Modeled Residue Count: 603
Deposited Residue Count: 684
Unique protein chains: 3

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
7B11 light chain	A	211	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
7B11 heavy chain	B	219	Mus musculus	Mutation(s): 0

Find similar proteins by:

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Envelope glycoprotein B,Envelope glycoprotein B	C	254	Suid alphaherpesvirus 1	Mutation(s): 0 Gene Names: gB
UniProt
Find proteins for A0A1Q0AKY5 (Suid herpesvirus 1) Explore A0A1Q0AKY5 Go to UniProtKB: A0A1Q0AKY5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A0A1Q0AKY5
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.29 Å
R-Value Free: 0.310 (Depositor), 0.313 (DCC)
R-Value Work: 0.241 (Depositor), 0.249 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 128.907	α = 90
b = 128.907	β = 90
c = 194.914	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
SHELXD	phasing

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
	China	--

Revision History (Full details and data files)

Version 1.0: 2019-05-22
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-13
Changes: Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.