5VN3	Immune System	date	Apr 28, 2017
title	Cryo-Em Model Of B41 Sosip.664 In Complex With Soluble Cd4 ( Fragment Antigen Binding Variable Domain Of 17b
authors	G.Ozorowski, J.Pallesen, A.B.Ward
compound		source
Molecule: 17b Fab Light Chain Chain: L, N, O Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f
Molecule: Envelope Glycoprotein Gp160 Chain: A, B, D Engineered: Yes Mutation: Yes		Organism_scientific: Human Immunodeficiency Virus 1 Organism_taxid: 11676 Gene: Env Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f
Molecule: Envelope Glycoprotein Gp160 Chain: G, I, J Engineered: Yes Mutation: Yes		Organism_scientific: Human Immunodeficiency Virus 1 Organism_taxid: 11676 Variant: 9032-08.A1.4685 Gene: Env Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f
Molecule: T-Cell Surface Glycoprotein Cd4 Chain: C, E, F Synonym: T-Cell Surface Antigen T4leu-3 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Cd4 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f
Molecule: 17b Fab Heavy Chain Chain: H, K, M Engineered: Yes		Organism_scientific: Homo Sapiens Organism_taxid: 9606 Expression_system: Homo Sapiens Expression_system_taxid: 9606 Expression_system_cell_line: Hek293f
symmetry	Space Group: P 1	R_factor R_Free
crystal cell	length a length b length c angle alpha angle beta angle gamma 1.000 1.000 1.000 90.00 90.00 90.00
method	Electron Microscopy	resolution	3.70 Å
ligand	BMA, MAN, NAG	enzyme
Gene Ontology	Chain Function Process Component A, D, B F, C, E J, I, G
Primary reference	Open and closed structures reveal allostery and pliability in the HIV-1 envelope spike., Ozorowski G, Pallesen J, de Val N, Lyumkis D, Cottrell CA, Torres JL, Copps J, Stanfield RL, Cupo A, Pugach P, Moore JP, Wilson IA, Ward AB, Nature. 2017 Jul 20;547(7663):360-363. doi: 10.1038/nature23010. Epub 2017 Jul, 12. PMID:28700571

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (446 Kb) [Save to disk] Biological Unit Coordinates (5vn3.pdb1.gz) 425 Kb LPC: Ligand-Protein Contacts for 5VN3 CSU: Contacts of Structural Units for 5VN3 Retrieve 5VN3 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5VN3 from S2C, [Save to disk]

View 5VN3 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 5VN3

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5vn3_B] [5vn3_K] [5vn3_G] [5vn3_E] [5vn3_A] [5vn3_O] [5vn3_F] [5vn3_N] [5vn3_D] [5vn3_M] [5vn3_I] [5vn3_C] [5vn3_J] [5vn3_L] [5vn3_H] SWISS-PROT database: Domain organization of by SWISSPFAM

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