9E7D | pdb_00009e7d

Crystal structure of HIV-1 RRE SLII A31C mutant in complex with Fab BL3-6

• PDB DOI: https://doi.org/10.2210/pdb9E7D/pdb
• NAKB: 9E7D

• Classification: RNA
• Organism(s): Human immunodeficiency virus 1, Homo sapiens
• 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): Other government

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free: 
  0.329 (Depositor), 0.332 (DCC) 
• R-Value Work: 
  0.246 (Depositor), 0.258 (DCC) 
• R-Value Observed: 
  0.250 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of HIV-1 RRE SLII A31C mutant in complex with Fab BL3-6

Ojha, M., Koirala, D.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: native gel electrophoresis

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 142.8 kDa 
• Atom Count: 9,736 
• Modeled Residue Count: 1,026 
• Deposited Residue Count: 1,040 
• Unique protein chains: 2
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab heavy chain	C [auth H], E [auth A]	233	Homo sapiens	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
BL3-6 Fab light chain	D [auth L], F [auth B]	215	Homo sapiens	Mutation(s): 0

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Rev response element SLIIc	A [auth R], B [auth C]	72	Human immunodeficiency virus 1

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.11 Å
• R-Value Free:  0.329 (Depositor), 0.332 (DCC) 
• R-Value Work:  0.246 (Depositor), 0.258 (DCC) 
• R-Value Observed: 0.250 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.874	α = 63.17
b = 75.871	β = 71.85
c = 83.516	γ = 77.75

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-05-28 
Deposition Author(s): Ojha, M., Koirala, D.

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Funding Organization	Location	Grant Number
Other government	United States	NA

Revision History  

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