Biological Assembly 1  

 3D View: Structure

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB Pseudo Symmetry: Cyclic - C2  (3D View)
Pseudo Stoichiometry: Homo 2-mer -A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 77032.56 
• Atom Count: 5321 
• Residue Count: 621 
• Unique protein chains: 2
• Unique nucleic acid chains: 2

1LEI

The kB DNA sequence from the HLV-LTR functions as an allosteric regulator of HIV transcription

• DOI: 10.2210/pdb1LEI/pdb
• NDB: PD0310

• Classification: TRANSCRIPTION/DNA
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2002-04-09 Released: 2003-04-15 
• Deposition Author(s): Chen-Park, F., Huang, D.B., Ghosh, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.284 
• R-Value Work: 0.250 

Literature

The kB DNA sequence from the HIV Long Terminal Repeat functions as an allosteric regulator of HIV transcription

Chen-Park, F.E., Huang, D.B., Noro, B., Thanos, D., Ghosh, G.

(2002) J.Biol.Chem. 277: 24701-24708

• PubMed: 11970949 
• DOI: 10.1074/jbc.M200007200


• PubMed Abstract: 
  

NF-kappaB is an inducible transcription factor involved in the immune response, inflammation, and viral transcription. To address how the two NF-kappaB and three Sp1 binding sites of the human immunodeficiency virus (HIV) long terminal repeat (LTR) control multiple activator assembly and transcription, we first observed and compared unique conformations between the crystallographic structure of the NF-kappaB p50.p65 heterodimer bound to the uPA-kappaB target site to that of the p50.p65.HIV-kappaB complex. Next, cooperativity between two NF-kappaB molecules bound to tandem HIV-kappaB sequences was measured as well as that of NF-kappaB and transcription factor Sp1 when bound to adjacent sites. The cooperativity of hybrid HIV-LTR enhancers was measured with the 3' kappaB site converted to uPA-kappaB or to interferon beta gene enhancer kappaB. The hybrids were defective in transcriptional activator assembly and less active transcriptionally. These functional differences correlate with observed conformational differences and demonstrate that distinct kappaB DNA sequences function as allosteric regulators in a gene-specific manner.

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Organizational Affiliation: 

Department of Biology, University of California, San Diego, La Jolla, California 92093-0359, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
NUCLEAR FACTOR NF-KAPPA-B P65 SUBUNIT	A	274	Mus musculus	Mutation(s): 0  Gene Names: Rela (Nfkb3)
Find proteins for Q04207 (Mus musculus) Go to UniProtKB:  Q04207

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
NUCLEAR FACTOR NF-KAPPA-B P50 SUBUNIT	B	313	Mus musculus	Mutation(s): 0  Gene Names: Nfkb1
Find proteins for P25799 (Mus musculus) Go to UniProtKB:  P25799

Entity ID: 1
Molecule	Chains	Length	Organism
5'-D(*CP*TP*CP*AP*GP*GP*GP*AP*AP*AP*GP*TP*AP*CP*AP*GP*A)-3'	C	17	N/A

Entity ID: 2
Molecule	Chains	Length	Organism
5'-D(*TP*CP*TP*GP*5ITP*AP*CP*5ITP*5ITP*5ITP*CP*CP*CP*TP*GP*AP*G)-3'	D	17	N/A

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
5IU	D	DNA LINKING	C9 H12 I N2 O8 P		DU

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DNA	Kd: 0.8 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.7 Å
• R-Value Free: 0.284 
• R-Value Work: 0.250 
• Space Group: C 2 2 2

Unit Cell:

Length (Å)	Angle (°)
a = 137.131	α = 90.00
b = 179.697	β = 90.00
c = 97.068	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
CNS	refinement
DENZO	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2002-04-09 
• Released Date: 2003-04-15 
• Deposition Author(s): Chen-Park, F., Huang, D.B., Ghosh, G.

Revision History 

• Version 1.0: 2003-04-15
  Type: Initial release
• Version 1.1: 2008-04-28
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance