1P71

Anabaena HU-DNA corcrystal structure (TR3)

• PDB DOI:  https://doi.org/10.2210/pdb1P71/pdb
• NAKB: 1P71

• Classification: DNA Binding Protein/DNA
• Organism(s): Anabaena sp.
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-04-30 Released: 2003-05-13 
• Deposition Author(s): Swinger, K.S., Lemberg, K.M., Zhang, Y., Rice, P.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.288 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 

Literature

Flexible DNA bending in HU-DNA cocrystal structures

Swinger, K.S., Lemberg, K.M., Zhang, Y., Rice, P.A.

(2003) EMBO J 22: 3749-3760

• PubMed: 12853489 
• DOI: https://doi.org/10.1093/emboj/cdg351
• Primary Citation of Related Structures:  
  1P51, 1P71, 1P78


• PubMed Abstract: 
  

HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles ( approximately 105-140 degrees ). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU-DNA and IHF-DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU's role as an architectural cofactor in many different systems that may require differing geometries.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, The University of Chicago, 920 East 58th Street, Chicago, IL 60637, USA.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 32.94 kDa 
• Atom Count: 2,395 
• Modelled Residue Count: 227 
• Deposited Residue Count: 230 
• Unique protein chains: 1
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA-binding protein HU	C [auth A], D [auth B]	94	Anabaena sp.	Mutation(s): 0  Gene Names: HUP OR HANA OR ASR3935
UniProt
Find proteins for P05514 (Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)) Explore P05514  Go to UniProtKB:  P05514

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*CP*TP*TP*AP*TP*CP*AP*AP*TP*TP*TP*GP*TP*TP*GP*CP*AP*CP*C)-3'	A [auth C], B [auth D]	21	N/A

Small Molecules

Binding Affinity Annotations
ID	Source	Binding Affinity
DNA	PDBBind:  1P71	Kd: 3.5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.288 
• R-Value Work: 0.244 
• R-Value Observed: 0.246 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.441	α = 90
b = 93.062	β = 90
c = 100.342	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2003-05-13 
Deposition Author(s): Swinger, K.S., Lemberg, K.M., Zhang, Y., Rice, P.A.

Revision History  

• Version 1.0: 2003-05-13
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.3: 2023-08-16
  Changes: Data collection, Database references, Refinement description