3H3B Immune System date Apr 16, 2009
title Crystal Structure Of The Single-Chain Fv (Scfv) Fragment Of Erbb2 Antibody Cha21 In Complex With Residues 1-192 Of Erbb Extracellular Domain
authors H.Zhou, Y.Liu, L.Niu, J.Zhu, M.Teng
compound source
Molecule: Receptor Tyrosine-Protein Kinase Erbb-2
Chain: A, B
Fragment: Extracellular Domain, Unp Residues 23-214
Synonym: P185erbb2, C-Erbb-2, Neu Proto-Oncogene, Tyrosine Type Cell Surface Receptor Her2, Mln 19;
Ec: 2.7.10.1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Erbb2
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami B
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pgex-4t-1

Molecule: Anti-Erbb2 Antibody Cha21
Chain: C, D
Fragment: The Single-Chain Fv (Scfv) Fragment
Engineered: Yes

Organism_scientific: Mus Musculus
Organism_common: Mouse
Organism_taxid: 10090
Strain: Balbc
Gene: Scfv Of Murine Antibody A21
Expression_system: Cricetulus Griseus
Expression_system_taxid: 10029
Expression_system_cell_line: Cho Cells
Expression_system_organ: Ovary
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pee14
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.255
crystal
cell
length a length b length c angle alpha angle beta angle gamma
82.177 87.200 108.520 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.45 Å
ligand
enzyme Transferase E.C.2.7.10.1 BRENDA
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural Insights into the Down-regulation of Overexpressed p185her2/neu Protein of Transformed Cells by the Antibody chA21., Zhou H, Zha Z, Liu Y, Zhang H, Zhu J, Hu S, Shen G, Cheng L, Niu L, Greene MI, Teng M, Liu J, J Biol Chem. 2011 Sep 9;286(36):31676-83. Epub 2011 Jun 16. PMID:21680730
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (144 Kb) [Save to disk]
  • Biological Unit Coordinates (3h3b.pdb1.gz) 70 Kb
  • Biological Unit Coordinates (3h3b.pdb2.gz) 70 Kb
  • CSU: Contacts of Structural Units for 3H3B
  • Structure Factors (1507 Kb)
  • Retrieve 3H3B in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3H3B from S2C, [Save to disk]
  • Re-refined 3h3b structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3H3B 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 3H3B
  • 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 3H3B, from MSDmotif at EBI
  • Fold representative 3h3b from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3h3b_D] [3h3b] [3h3b_C] [3h3b_A] [3h3b_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Alignments of the sequence of 3H3B with the sequences similar proteins can be viewed for 3H3B's classification at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification at ProtoMap. Click on the Cluster number.
  • Other resources with information on 3H3B
  • Community annotation for 3H3B at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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