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- PDB-2nvu: Structure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trappe... -

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Basic information

Entry
Database: PDB / ID: 2nvu
TitleStructure of APPBP1-UBA3~NEDD8-NEDD8-MgATP-Ubc12(C111A), a trapped ubiquitin-like protein activation complex
Components
  • Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera
  • NEDD8-activating enzyme E1 regulatory subunit
  • NEDD8-conjugating enzyme Ubc12
  • NEDD8
KeywordsPROTEIN TURNOVER / LIGASE / Multifunction macromolecular complex / Ubiquitin / NEDD8 / E1 / E2 / ATP / Conformational change / thioester / switch / adenylation
Function / homology
Function and homology information


E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / regulation of proteolysis / mitotic DNA replication checkpoint signaling / protein neddylation ...E2 NEDD8-conjugating enzyme / NEDD8 conjugating enzyme activity / E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / regulation of proteolysis / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / anatomical structure morphogenesis / regulation of neuron apoptotic process / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / Iron uptake and transport / protein modification process / modification-dependent protein catabolic process / protein localization / protein tag activity / ubiquitin-protein transferase activity / UCH proteinases / positive regulation of neuron apoptotic process / Antigen processing: Ubiquitination & Proteasome degradation / Cargo recognition for clathrin-mediated endocytosis / Neddylation / ubiquitin-dependent protein catabolic process / neuron apoptotic process / regulation of apoptotic process / protein ubiquitination / regulation of cell cycle / protein heterodimerization activity / DNA damage response / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / signal transduction / protein-containing complex / proteolysis / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
NEDD8-activating enzyme E1 regulatory subunit APP-BP1 / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / Ubiquitin activating enzyme, alpha domain superfamily / Nedd8-like ubiquitin / Ubiquitin-activating enzyme E1, Cys active site ...NEDD8-activating enzyme E1 regulatory subunit APP-BP1 / Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 / E2 binding / NEDD8-activating enzyme E1 catalytic subunit / E2 binding domain / E2_bind / Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 / Ubiquitin activating enzyme, alpha domain superfamily / Nedd8-like ubiquitin / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme active site. / ThiF/MoeB/HesA family / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A / Ubiquitin Conjugating Enzyme / Ubiquitin Conjugating Enzyme / Ubiquitin-conjugating enzyme, active site / Ubiquitin-conjugating (UBC) active site signature. / Ubiquitin-conjugating enzyme E2, catalytic domain homologues / Ubiquitin-conjugating enzyme E2 / Ubiquitin-conjugating enzyme / Ubiquitin-conjugating (UBC) core domain profile. / Ubiquitin-conjugating enzyme/RWD-like / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Periplasmic binding protein-like II / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / D-Maltodextrin-Binding Protein; domain 2 / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Arc Repressor Mutant, subunit A / Ubiquitin-like domain superfamily / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / NEDD8-conjugating enzyme Ubc12 / NEDD8-activating enzyme E1 regulatory subunit / NEDD8 / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHuang, D.T. / Hunt, H.W. / Zhuang, M. / Ohi, M.D. / Holton, J.M. / Schulman, B.A.
CitationJournal: Nature / Year: 2007
Title: Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity.
Authors: Huang, D.T. / Hunt, H.W. / Zhuang, M. / Ohi, M.D. / Holton, J.M. / Schulman, B.A.
History
DepositionNov 13, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 30, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE ENTITY 2 (CHAIN B) CONTAINS TWO DIFFERENT PROTEINS: MALTOSE BINDING PROTEIN (MBP, RESIDUES ...SEQUENCE ENTITY 2 (CHAIN B) CONTAINS TWO DIFFERENT PROTEINS: MALTOSE BINDING PROTEIN (MBP, RESIDUES 1001-1368) AND NEDD8-ACTIVATING ENZYME E1 CATALYTIC SUBUNIT (UBA3, RESIDUES 2012-2442) CONNECTED BY THE ALA-ALA-ALA LINKER (RESIDUES 1369-1371). THERE IS NO DATABASE SEQUENCE AVAILABLE AT UNIPROT FOR MBP AT THE TIME OF DEPOSITION. AUTHORS STATE THAT THE MBP SEQUENCE IS AVAILABLE ONLY IN NCBI DATABASE WITH ACCESSION NUMBERS AAB86559 OR 1R6Z_P. PROTEIN UBA3 HAS A DATABASE SEQUENCE REFERENCE IN UNIPROT WHICH IS STATED IN DBREF. ENTITY 2 ALSO CONTAINS N-TERMINAL CLONING ARTIFACT (RESIDUES MET-LYS-LEU, RESIDUES 998-1000) AND THREE MUTATIONS (E1360A,K1363A,D1364A). THE C-TERMINAL CARBON ATOM OF CHAIN "J" (RESIDUE 76) FORMS A THIOESTER LINK WITH CHAIN "B" BY THE SIDE CHAIN ATOM SG OF RESIDUE 2216 OF THE UBA3 MOIETY

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NEDD8-activating enzyme E1 regulatory subunit
B: Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera
C: NEDD8-conjugating enzyme Ubc12
I: NEDD8
J: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,8938
Polymers188,2965
Non-polymers5973
Water81145
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.494, 156.494, 190.485
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 4 types, 5 molecules ABCIJ

#1: Protein NEDD8-activating enzyme E1 regulatory subunit / Amyloid protein-binding protein 1 / Amyloid beta precursor protein-binding protein 1 / 59 kDa / APP- ...Amyloid protein-binding protein 1 / Amyloid beta precursor protein-binding protein 1 / 59 kDa / APP-BP1 / Protooncogene protein 1 / HPP1


Mass: 60459.227 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPBP1 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q13564
#2: Protein Maltose binding protein/NEDD8-activating enzyme E1 catalytic subunit chimera / MBP / Ubiquitin-activating enzyme 3 / NEDD8-activating enzyme E1C / Ubiquitin-activating enzyme E1C


Mass: 89332.766 Da / Num. of mol.: 1 / Fragment: Residues 33-463
Source method: isolated from a genetically manipulated source
Details: Fusion protein. Maltose binding protein (residues 1001-1371), and the NEDD8-activating enzyme E1 catalytic subunit (residues 2012-2442) is from a human source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE1C, UBA3 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD
References: UniProt: Q8TBC4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein NEDD8-conjugating enzyme Ubc12 / Ubiquitin-conjugating enzyme E2 M / NEDD8 protein ligase / NEDD8 carrier protein


Mass: 20665.666 Da / Num. of mol.: 1 / Mutation: del(S16-T20), C111A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2M, UBC12 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD
References: UniProt: P61081, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#4: Protein NEDD8 / / Ubiquitin-like protein Nedd8 / Neddylin


Mass: 8919.289 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)GOLD / References: UniProt: Q15843

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Non-polymers , 4 types, 48 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE / Adenosine triphosphate


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 45 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.57 Å3/Da / Density % sol: 65.59 %
Description: AUTHORS SCREENED >900 CRYSTALS AND USED ALL THREE BEAMLINES TO OBTAIN NECESSARY INFORMATION FOR FINAL STRUCTURE DETERMINATION FROM SINGLE CRYSTAL AT APS BEAMLINE 22-ID
Crystal growTemperature: 291 K / pH: 7
Details: 17% v/v PEG 3350, 0.1 M HEPES pH 7.0, 0.2 M Disodium tartrate, VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 7.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9793
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 16, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 65807 / % possible obs: 95.7 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Rsym value: 0.134 / Net I/σ(I): 25.7

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1R4M, 1Y8X

1r4m

1y8x


Resolution: 2.8→50 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3298 4.9 %RANDOM
Rwork0.241 ---
obs0.241 65807 98.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.29 Å2
Displacement parametersBiso mean: 83.78 Å2
Baniso -1Baniso -2Baniso -3
1--14.199 Å2-11.808 Å20 Å2
2---14.199 Å20 Å2
3---28.397 Å2
Refinement stepCycle: LAST / Resolution: 2.8→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13012 0 33 45 13090
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.44
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CNS_TOPPAR:ION.PARAM
X-RAY DIFFRACTION3CNS_TOPPAR:WATER_REP.PARAM
X-RAY DIFFRACTION4ATP.PAR

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