1R4M	Cell Cycle	date	Oct 07, 2003
title	Appbp1-Uba3-Nedd8, An E1-Ubiquitin-Like Protein Complex
authors	H.Walden, M.S.Podgorski, J.M.Holton, B.A.Schulman
compound		source
Molecule: Amyloid Beta Precursor Protein-Binding Protein 1 Chain: A, C, E, G Synonym: Appbp1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-Activating Enzyme E1c Chain: B, D, F, H Synonym: Uba3 Engineered: Yes Mutation: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Ubiquitin-Like Protein Nedd8 Chain: I, J, K, L Synonym: Nedd8 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Nedd8 Expression_system: Escherichia Coli Expression_system_taxid: 562
symmetry	Space Group: P 21 21 21	R_factor 0.240 R_Free 0.280
crystal cell	length a length b length c angle alpha angle beta angle gamma 135.400 198.900 209.800 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.00 Å
ligand	ZN	enzyme
related structures	by homologous chain: 1TT5, 1XT9
Gene Ontology	Chain Function Process Component A, E, C, G F, B, H, D J, K, I, L
Primary reference	The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1., Walden H, Podgorski MS, Huang DT, Miller DW, Howard RJ, Minor DL Jr, Holton JM, Schulman BA, Mol Cell 2003 Dec;12(6):1427-37. PMID:14690597

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (589 Kb) [Save to disk] Biological Unit Coordinates (1r4m.pdb1.gz) 151 Kb Biological Unit Coordinates (1r4m.pdb2.gz) 151 Kb Biological Unit Coordinates (1r4m.pdb3.gz) 152 Kb Biological Unit Coordinates (1r4m.pdb4.gz) 150 Kb LPC: Ligand-Protein Contacts for 1R4M CSU: Contacts of Structural Units for 1R4M Likely Quarternary Molecular Structure file(s) for 1R4M Retrieve 1R4M in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 1R4M from S2C, [Save to disk]

View 1R4M 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 1R4M

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute 3D motif for 1R4M, from MSDmotif at EBI Classification of representative domains in scop (Structural Classification of Proteins)     - Domain d1r4ma_, region A [Jmol] [rasmolscript] [script source]     - Domain d1r4mb_, region B [Jmol] [rasmolscript] [script source]     - Domain d1r4mc_, region C [Jmol] [rasmolscript] [script source]     - Domain d1r4md_, region D [Jmol] [rasmolscript] [script source]     - Domain d1r4me_, region E [Jmol] [rasmolscript] [script source]     - Domain d1r4mf_, region F [Jmol] [rasmolscript] [script source]     - Domain d1r4mg_, region G [Jmol] [rasmolscript] [script source]     - Domain d1r4mh_, region H [Jmol] [rasmolscript] [script source]     - Domain d1r4mi_, region I [Jmol] [rasmolscript] [script source]     - Domain d1r4mj_, region J [Jmol] [rasmolscript] [script source]     - Domain d1r4mk_, region K [Jmol] [rasmolscript] [script source]     - Domain d1r4ml_, region L [Jmol] [rasmolscript] [script source] 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: [1r4m_C] [1r4m_H] [1r4m_K] [1r4m_L] [1r4m_E] [1r4m_G] [1r4m_D] [1r4m_A] [1r4m_J] [1r4m] [1r4m_I] [1r4m_F] [1r4m_B] SWISS-PROT database: [Q15843] [Q8TBC4] [Q13564] Domain organization of [NEDD8_HUMAN] [UBA3_HUMAN] [ULA1_HUMAN] by SWISSPFAM Domains found in 1R4M: [E2_bind] [UBQ ] by SMART

Other resources with information on 1R4M

Community annotation for 1R4M 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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