4NZG | pdb_00004nzg

Crystal Structure of the N-terminal domain of Moloney murine leukemia virus integrase, Northeast Structural Genomics Consortium Target OR3

PDB DOI: https://doi.org/10.2210/pdb4NZG/pdb

Classification: VIRAL PROTEIN
Organism(s): Moloney murine leukemia virus isolate Shinnick
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2013-12-12 Released: 2014-02-05
Deposition Author(s): Guan, R., Jiang, M., Janjua, H., Maglaqui, M., Zhao, L., Xiao, R., Acton, T.B., Everett, J.K., Roth, M., Montelione, G.T., Northeast Structural Genomics Consortium (NESG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free:
0.265 (Depositor), 0.268 (DCC)
R-Value Work:
0.234 (Depositor), 0.238 (DCC)
R-Value Observed:
0.236 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.3 of the entry. See complete history.

Literature

X-ray crystal structure of the N-terminal region of Moloney murine leukemia virus integrase and its implications for viral DNA recognition.

Guan, R., Aiyer, S., Cote, M.L., Xiao, R., Jiang, M., Acton, T.B., Roth, M.J., Montelione, G.T.

(2017) Proteins 85: 647-656

PubMed: 28066922 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1002/prot.25245
Primary Citation Related Structures:
3NNQ, 4NZG

PubMed Abstract:
The retroviral integrase (IN) carries out the integration of a dsDNA copy of the viral genome into the host DNA, an essential step for viral replication. All IN proteins have three general domains, the N-terminal domain (NTD), the catalytic core domain, and the C-terminal domain. The NTD includes an HHCC zinc finger-like motif, which is conserved in all retroviral IN proteins. Two crystal structures of Moloney murine leukemia virus (M-MuLV) IN N-terminal region (NTR) constructs that both include an N-terminal extension domain (NED, residues 1-44) and an HHCC zinc-finger NTD (residues 45-105), in two crystal forms are reported. The structures of IN NTR constructs encoding residues 1-105 (NTR _1-105 ) and 8-105 (NTR _8-105 ) were determined at 2.7 and 2.15 Å resolution, respectively and belong to different space groups. While both crystal forms have similar protomer structures, NTR _1-105 packs as a dimer and NTR _8-105 packs as a tetramer in the asymmetric unit. The structure of the NED consists of three anti-parallel β-strands and an α-helix, similar to the NED of prototype foamy virus (PFV) IN. These three β-strands form an extended β-sheet with another β-strand in the HHCC Zn ²⁺ binding domain, which is a unique structural feature for the M-MuLV IN. The HHCC Zn ²⁺ binding domain structure is similar to that in HIV and PFV INs, with variations within the loop regions. Differences between the PFV and MLV IN NEDs localize at regions identified to interact with the PFV LTR and are compared with established biochemical and virological data for M-MuLV. Proteins 2017; 85:647-656. © 2016 Wiley Periodicals, Inc.

Organizational Affiliation

Center for Advanced Biotechnology and Medicine, Rutgers, The State University of New Jersey, Piscataway, New Jersey, 08854.

Macromolecule Content

Total Structure Weight: 48.83 kDa
Atom Count: 3,243
Modeled Residue Count: 372
Deposited Residue Count: 400
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Integrase p46	A, B, C, D	100	Moloney murine leukemia virus isolate Shinnick	Mutation(s): 0 Gene Names: gag-pol
UniProt
Find proteins for P03355 (Moloney murine leukemia virus (isolate Shinnick)) Explore P03355 Go to UniProtKB: P03355
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P03355
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DTT Query on DTT Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain S [auth D] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain N [auth B] SDF format, chain M [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain S [auth D] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth B] mmCIF format, chain S [auth D] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth B] mmCIF format, chain G [auth A]	G [auth A] H [auth A] I [auth A] L [auth B] M [auth B] G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], P [auth C], Q [auth C], S [auth D]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain S [auth D]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain T [auth D] SDF format, chain O [auth C] SDF format, chain J [auth B] SDF format, chain E [auth A] MOL2 format, chain T [auth D] MOL2 format, chain O [auth C] MOL2 format, chain J [auth B] MOL2 format, chain E [auth A] mmCIF format, chain T [auth D] mmCIF format, chain O [auth C] mmCIF format, chain J [auth B] mmCIF format, chain E [auth A]	E [auth A], J [auth B], O [auth C], T [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Focus chain T [auth D]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain R [auth D] SDF format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain R [auth D] MOL2 format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain R [auth D] mmCIF format, chain F [auth A]	F [auth A], K [auth B], R [auth D]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain R [auth D]