4R2G Immune System date Aug 11, 2014
title Crystal Structure Of Pgt124 Fab Bound To Hiv-1 Jrcsf Gp120 C Cd4
authors F.Garces, I.A.Wilson
compound source
Molecule: Surface Protein Gp160
Chain: E, O, A, K
Synonym: Env Polyprotein,Env Polyprotein
Engineered: Yes
Organism_scientific: Human Immunodeficiency Virus Type 1 Gr Subtype B;
Organism_common: Hiv-1
Organism_taxid: 11688
Strain: Isolate Jrcsf
Gene: Env
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: 293 Freestyle

Molecule: T-Cell Surface Glycoprotein Cd4
Chain: F, B, H, L
Synonym: T-Cell Surface Antigen T4leu-3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cd4
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Pgt124 Light Chain
Chain: P, C, I, M
Synonym: Ig Lambda Chain C Region Dot,Ig Lambda Chain C Reg Ig Lambda-3 Chain C Regions;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human, Human
Organism_taxid: 9606
Gene: Igl@, Iglc3
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: 293 Freestyle

Molecule: Pgt124 Heavy Chain
Chain: Q, D, J, N
Synonym: Immunoglobulin Gamma-1 Heavy Chain Nie
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human, Human
Organism_taxid: 9606
Gene: Igh@
Expression_system: Homo Sapiens
Expression_system_common: Human
Expression_system_taxid: 9606
Expression_system_cell_line: 293 Freestyle
symmetry Space Group: P 21 21 21
R_factor 0.207 R_Free 0.263
crystal
cell
length a length b length c angle alpha angle beta angle gamma
164.406 165.438 229.712 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.28 Å
ligand BMA, CL, GOL, MAN, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, O, K, E


H, F, L, B


Primary referenceStructural Evolution of Glycan Recognition by a Family of Potent HIV Antibodies., Garces F, Sok D, Kong L, McBride R, Kim HJ, Saye-Francisco KF, Julien JP, Hua Y, Cupo A, Moore JP, Paulson JC, Ward AB, Burton DR, Wilson IA, Cell. 2014 Sep 25;159(1):69-79. doi: 10.1016/j.cell.2014.09.009. PMID:25259921
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (601 Kb) [Save to disk]
  • Biological Unit Coordinates (4r2g.pdb1.gz) 155 Kb
  • Biological Unit Coordinates (4r2g.pdb2.gz) 154 Kb
  • Biological Unit Coordinates (4r2g.pdb3.gz) 154 Kb
  • Biological Unit Coordinates (4r2g.pdb4.gz) 155 Kb
  • LPC: Ligand-Protein Contacts for 4R2G
  • CSU: Contacts of Structural Units for 4R2G
  • Structure Factors (1655 Kb)
  • Retrieve 4R2G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4R2G from S2C, [Save to disk]
  • Re-refined 4r2g structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4R2G in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 4R2G
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4R2G, from MSDmotif at EBI
  • Fold representative 4r2g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4r2g_I] [4r2g_A] [4r2g_E] [4r2g_D] [4r2g_Q] [4r2g_N] [4r2g_C] [4r2g_L] [4r2g_J] [4r2g_O] [4r2g_M] [4r2g] [4r2g_F] [4r2g_P] [4r2g_B] [4r2g_K] [4r2g_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4R2G: [IG_like] [IGv ] by SMART
  • Other resources with information on 4R2G
  • Community annotation for 4R2G at PDBWiki (http://pdbwiki.org)

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