7N9X

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

PDB DOI: https://doi.org/10.2210/pdb7N9X/pdb

Classification: VIRAL PROTEIN/IMMUNE SYSTEM
Organism(s): Human immunodeficiency virus 1, Lama glama, Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2021-06-18 Released: 2022-06-22
Deposition Author(s): Gerber, E.E., Digianantonio, K.M., Tripler, T.N., Smaga, S.S., Summers, B.J., Xiong, Y.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.270
R-Value Work: 0.245

wwPDB Validation 3D Report Full Report

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

Literature

CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions

Gerber, E.E., Digianantonio, K.M., Tripler, T.N., Smaga, S.S., Summers, B.J., Xiong, Y.

To be published.

Macromolecule Content

Total Structure Weight: 164.51 kDa
Atom Count: 11,458
Modelled Residue Count: 1,490
Deposited Residue Count: 1,502
Unique protein chains: 5

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein	A [auth BBB], B [auth CCC], C [auth AAA]	222	Human immunodeficiency virus 1	Mutation(s): 0 Gene Names: gag
UniProt
Find proteins for B6DRA0 (Human immunodeficiency virus 1) Explore B6DRA0 Go to UniProtKB: B6DRA0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B6DRA0
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	D [auth FFF]	115	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	E [auth EEE]	112	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Nanobody	F [auth DDD]	114	Lama glama	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	G [auth GGG], H [auth HHH], I [auth III]	165	Homo sapiens	Mutation(s): 0 Gene Names: PPIA, CYPA EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens) Explore P62937 Go to UniProtKB: P62937
PHAROS: P62937 GTEx: ENSG00000196262
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P62937
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.51 Å
R-Value Free: 0.270
R-Value Work: 0.245
Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.95	α = 90
b = 137.85	β = 90
c = 313.832	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2022-06-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	P50GM082251
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	F32 GM131426 01A1