1M4U Hormone Growth Factor date Jul 03, 2002
title Crystal Structure Of Bone Morphogenetic Protein-7 (Bmp-7) In With The Secreted Antagonist Noggin
authors J.Groppe, J.Greenwald, E.Wiater, J.Rodriguez-Leon, A.N.Economide W.Kwiatkowski, M.Affolter, W.W.Vale, J.C.Izpisua-Belmonte, S.Ch
compound source
Molecule: Bone Morphogenetic Protein-7
Chain: L
Synonym: Bmp-7, Osteogenic Protein 1, Op-1
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Bmp7
Expression_system: Cricetulus Griseus
Expression_system_common: Chinese Hamster
Expression_system_taxid: 10029
Expression_system_cell: Ovary Cells
Expression_system_vector_type: Baculovirus
Other_details: Dhfr-

Molecule: Noggin
Chain: A
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Nog
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: W3110 Laciq
Expression_system_plasmid: Prg301
Other_details: High Copy Number Derivative Of Pbr322 With A Promoter
symmetry Space Group: P 41 21 2
R_factor 0.241 R_Free 0.273
crystal
cell
length a length b length c angle alpha angle beta angle gamma
99.834 99.834 150.327 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.42 Å
ligand NAG enzyme
related structures by homologous chain: 1BMP, 1LXI
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceStructural basis of BMP signalling inhibition by the cystine knot protein Noggin., Groppe J, Greenwald J, Wiater E, Rodriguez-Leon J, Economides AN, Kwiatkowski W, Affolter M, Vale WW, Belmonte JC, Choe S, Nature 2002 Dec 12;420(6916):636-42. PMID:12478285
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (60 Kb) [Save to disk]
  • Biological Unit Coordinates (1m4u.pdb1.gz) 104 Kb
  • LPC: Ligand-Protein Contacts for 1M4U
  • CSU: Contacts of Structural Units for 1M4U
  • Likely Quarternary Molecular Structure file(s) for 1M4U
  • Structure Factors (207 Kb)
  • Retrieve 1M4U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M4U from S2C, [Save to disk]
  • Re-refined 1m4u structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1M4U 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 1M4U
  • 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 1M4U, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m4ua_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m4ul_, region L [Jmol] [rasmolscript] [script source]
  • Fold representative 1m4u from FSSP and Dali (Families of Structurally Similar Proteins)
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1m4u] [1m4u_L] [1m4u_A]
  • SWISS-PROT database: [P18075] [Q13253]
  • Domain organization of [BMP7_HUMAN] [NOGG_HUMAN] by SWISSPFAM
  • Domain found in 1M4U: [TGFB ] by SMART
  • Alignments of the sequence of 1M4U with the sequences similar proteins can be viewed for 1M4U's classification [BMP7_HUMAN] [NOGG_HUMAN] 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 [BMP7_HUMAN] [NOGG_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1M4U
  • Community annotation for 1M4U 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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