9E7E | pdb_00009e7e

Crystal structure of HIV-1 RRE SLII A31CG39C mutant in complex with Fab BL3-6

PDB DOI: https://doi.org/10.2210/pdb9E7E/pdb
NAKB: 9E7E

Classification: RNA
Organism(s): Homo sapiens, Human immunodeficiency virus 1
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2024-11-01 Released: 2025-05-28
Deposition Author(s): Ojha, M., Koirala, D.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.293 (Depositor), 0.292 (DCC)
R-Value Work:
0.250 (Depositor), 0.251 (DCC)
R-Value Observed:
0.251 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Crystal structure of HIV-1 RRE SLII A31CG39C mutant in complex with Fab BL3-6

Ojha, M., Koirala, D.

To be published.

Macromolecule Content

Total Structure Weight: 285.44 kDa
Atom Count: 19,620
Modeled Residue Count: 2,052
Deposited Residue Count: 2,080
Unique protein chains: 2
Unique nucleic acid chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab heavy chain	A [auth H], D [auth A], H [auth D], K [auth G]	233	Homo sapiens	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: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab light chain	B [auth L], E [auth B], I [auth E], L [auth I]	215	Homo sapiens	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	Length	Organism	Image
Rev Response Element SLII A31C/G39C	C [auth R], F [auth C], G [auth F], J [auth O]	72	Human immunodeficiency virus 1
Sequence Annotations Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.293 (Depositor), 0.292 (DCC)
R-Value Work: 0.250 (Depositor), 0.251 (DCC)
R-Value Observed: 0.251 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 84.369	α = 77.48
b = 95.645	β = 76.34
c = 111.239	γ = 74.25

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHENIX	phasing

Structure Validation

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Entry History & Funding Information

Deposition Data

Released Date: 2025-05-28

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	U54AI170660-01/SUBK00019302

Revision History (Full details and data files)

Version 1.0: 2025-05-28
Type: Initial release

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.