4N9F Ligase Viral Protein date Oct 21, 2013
title Crystal Structure Of The Vif-Cbfbeta-Cul5-Elob-Eloc Pentamer
authors Y.Y.Guo, L.Y.Dong, Z.W.Huang
compound source
Molecule: Cullin-5
Chain: U, C, I, O, V, f, l, r, x, 3, 9, w
Fragment: Unp Residues 12-321
Synonym: Cul-5, Vasopressin-Activated Calcium-Mobilizing Re Vacm-1;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cul5, Vacm1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Elongation Factor B Polypeptide 1
Chain: Y, E, K, Q, Z, h, n, t, z, 5, T, B
Synonym: Elongin 15 Kda Subunit, Elongin-C, Eloc, Rna Polym Transcription Factor Siii Subunit C, Siii P15;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eloc, Tceb1
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Transcription Elongation Factor B Polypeptide 2
Chain: X, D, J, P, W, g, m, s, y, 4, e, H
Fragment: Unp Residues 1-102
Synonym: Elongin 18 Kda Subunit, Elongin-B, Elob, Rna Polym Transcription Factor Siii Subunit B, Siii P18;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Elob, Tceb2
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Core-Binding Factor Subunit Beta
Chain: a, F, L, R, c, I, o, u, 0, 6, k, N
Fragment: Unp Residues 1-170
Synonym: Cbf-Beta, Polyomavirus Enhancer-Binding Protein 2 Subunit, Pea2-Beta, Pebp2-Beta, Sl3-3 Enhancer Factor 1 Sub Sl3akv Core-Binding Factor Beta Subunit;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Cbfb, Cbfbeta
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Virion Infectivity Factor
Chain: b, G, M, S, d, j, p, v, 1, 7, q, 2
Fragment: Unp Residues 1-176
Engineered: Yes

Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Vif
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1
R_factor 0.262 R_Free 0.324
crystal
cell
length a length b length c angle alpha angle beta angle gamma
103.925 204.002 247.866 65.51 90.28 90.50
method X-Ray Diffractionresolution 3.30 Å
ligand ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
06


B, Q


F, L, R


I, U, C, O


J, D, P


K


N


S, 7, 2, 1, G, M


T, Y, E, Z, H, 5


V


W, 3, X, 9


a, u, k, c, i, o


d, j, v, q, b, p


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3186 Kb) [Save to disk]
  • Biological Unit Coordinates (4n9f.pdb1.gz) 285 Kb
  • Biological Unit Coordinates (4n9f.pdb2.gz) 285 Kb
  • Biological Unit Coordinates (4n9f.pdb3.gz) 284 Kb
  • Biological Unit Coordinates (4n9f.pdb4.gz) 284 Kb
  • Biological Unit Coordinates (4n9f.pdb5.gz) 284 Kb
  • Biological Unit Coordinates (4n9f.pdb6.gz) 287 Kb
  • Biological Unit Coordinates (4n9f.pdb7.gz) 283 Kb
  • Biological Unit Coordinates (4n9f.pdb8.gz) 283 Kb
  • Biological Unit Coordinates (4n9f.pdb9.gz) 286 Kb
  • LPC: Ligand-Protein Contacts for 4N9F
  • CSU: Contacts of Structural Units for 4N9F
  • Structure Factors (3110 Kb)
  • Retrieve 4N9F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 4N9F from S2C, [Save to disk]
  • Re-refined 4n9f structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 4N9F 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 4N9F
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 4N9F, from MSDmotif at EBI
  • Fold representative 4n9f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [4n9f_O] [4n9f_9] [4n9f_u] [4n9f_s] [4n9f_c] [4n9f_U] [4n9f_G] [4n9f_5] [4n9f_S] [4n9f_y] [4n9f_6] [4n9f_I] [4n9f_z] [4n9f_i] [4n9f_D] [4n9f_C] [4n9f_M] [4n9f_P] [4n9f_V] [4n9f_T] [4n9f_r] [4n9f_q] [4n9f_h] [4n9f_Q] [4n9f_m] [4n9f_R] [4n9f_B] [4n9f_e] [4n9f_j] [4n9f_L] [4n9f_k] [4n9f_g] [4n9f_1] [4n9f_d] [4n9f_N] [4n9f_x] [4n9f_0] [4n9f_n] [4n9f_W] [4n9f] [4n9f_v] [4n9f_p] [4n9f_7] [4n9f_K] [4n9f_o] [4n9f_f] [4n9f_Z] [4n9f_2] [4n9f_H] [4n9f_X] [4n9f_F] [4n9f_w] [4n9f_t] [4n9f_J] [4n9f_E] [4n9f_4] [4n9f_l] [4n9f_Y] [4n9f_a] [4n9f_3] [4n9f_b]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 4N9F: [Skp1] [UBQ ] by SMART
  • Other resources with information on 4N9F
  • Community annotation for 4N9F at PDBWiki (http://pdbwiki.org)

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