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- PDB-1r4m: APPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex -

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Basic information

Entry
Database: PDB / ID: 1r4m
TitleAPPBP1-UBA3-NEDD8, an E1-ubiquitin-like protein complex
Components
  • Ubiquitin-like protein NEDD8
  • amyloid beta precursor protein-binding protein 1
  • ubiquitin-activating enzyme E1C
KeywordsCELL CYCLE
Function / homology
Function and homology information


E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / regulation of postsynapse assembly / anatomical structure morphogenesis ...E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / NEDD8 transferase activity / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of proteolysis / regulation of postsynapse assembly / 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 tag activity / UCH proteinases / intracellular protein localization / Antigen processing: Ubiquitination & Proteasome degradation / Cargo recognition for clathrin-mediated endocytosis / Neddylation / neuron apoptotic process / ubiquitin-dependent protein catabolic process / regulation of apoptotic process / postsynapse / regulation of cell cycle / protein heterodimerization activity / ubiquitin protein ligase binding / regulation of transcription by RNA polymerase II / glutamatergic synapse / signal transduction / protein-containing complex / proteolysis / extracellular exosome / nucleoplasm / ATP binding / identical protein binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
NEDD8-activating enzyme E1, catalytic subunit / NEDD8-activating enzyme E1 regulatory subunit APP-BP1 / 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, catalytic subunit / NEDD8-activating enzyme E1 regulatory subunit APP-BP1 / 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 / THIF-type NAD/FAD binding fold / ThiF family / Ubiquitin-activating enzyme / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / : / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin-like (UB roll) / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Ubiquitin-like domain superfamily / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NEDD8-activating enzyme E1 regulatory subunit / Ubiquitin-like protein NEDD8 / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWalden, H. / Podgorski, M.S. / Holton, J.M. / Schulman, B.A.
CitationJournal: Mol.Cell / Year: 2003
Title: The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1.
Authors: Walden, H. / Podgorski, M.S. / Huang, D.T. / Miller, D.W. / Howard, R.J. / Minor, D.L. / Holton, J.M. / Schulman, B.A.
History
DepositionOct 7, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 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_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_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 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE The residues 600-608, 700-706, 800-802 and 900-917 of the chains B,D,F,H were modelled ...SEQUENCE The residues 600-608, 700-706, 800-802 and 900-917 of the chains B,D,F,H were modelled originally as alanines due to poor electron density. The residue names were assigned arbitrarily and the connectivity is unclear.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: amyloid beta precursor protein-binding protein 1
B: ubiquitin-activating enzyme E1C
I: Ubiquitin-like protein NEDD8
C: amyloid beta precursor protein-binding protein 1
D: ubiquitin-activating enzyme E1C
J: Ubiquitin-like protein NEDD8
E: amyloid beta precursor protein-binding protein 1
F: ubiquitin-activating enzyme E1C
K: Ubiquitin-like protein NEDD8
G: amyloid beta precursor protein-binding protein 1
H: ubiquitin-activating enzyme E1C
L: Ubiquitin-like protein NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)467,45316
Polymers467,19112
Non-polymers2624
Water00
1
A: amyloid beta precursor protein-binding protein 1
B: ubiquitin-activating enzyme E1C
I: Ubiquitin-like protein NEDD8


Theoretical massNumber of molelcules
Total (without water)116,7983
Polymers116,7983
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10210 Å2
ΔGint-36 kcal/mol
Surface area41170 Å2
MethodPISA
2
C: amyloid beta precursor protein-binding protein 1
D: ubiquitin-activating enzyme E1C
J: Ubiquitin-like protein NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8634
Polymers116,7983
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-69 kcal/mol
Surface area41110 Å2
MethodPISA
3
E: amyloid beta precursor protein-binding protein 1
F: ubiquitin-activating enzyme E1C
K: Ubiquitin-like protein NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,8634
Polymers116,7983
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10240 Å2
ΔGint-36 kcal/mol
Surface area41160 Å2
MethodPISA
4
G: amyloid beta precursor protein-binding protein 1
H: ubiquitin-activating enzyme E1C
L: Ubiquitin-like protein NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,9295
Polymers116,7983
Non-polymers1312
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10400 Å2
ΔGint-73 kcal/mol
Surface area41120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.400, 198.900, 209.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
amyloid beta precursor protein-binding protein 1 / APPBP1


Mass: 59829.652 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q13564
#2: Protein
ubiquitin-activating enzyme E1C / UBA3


Mass: 48394.219 Da / Num. of mol.: 4 / Mutation: C216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TBC4
#3: Protein
Ubiquitin-like protein NEDD8 / NEDD8


Mass: 8573.978 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15843
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: PEG10K, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7.6 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
110.5-10.7 %PEG100001reservoir
20.1 MTris1reservoir
30.4 M1reservoirNaCl
410 %PEG4001reservoir
55 mMdithiothreitol1reservoirpH8.0-8.5
650 mMTris1drop
7150 mM1dropNaCl
85 mM1dropMgCl2
95 mMATP1drop
105 mMdithiothreitol1droppH7.6
1115-30 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 16, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 113653 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1.8 / Redundancy: 24.6 % / Biso Wilson estimate: 84 Å2 / Rmerge(I) obs: 0.109 / Net I/σ(I): 17.1
Reflection shellResolution: 3→3.1 Å / Rmerge(I) obs: 0.596 / Mean I/σ(I) obs: 1.8 / % possible all: 99.9
Reflection
*PLUS
Num. obs: 113171 / Num. measured all: 2787084
Reflection shell
*PLUS
% possible obs: 99.9 %

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1NGV

1ngv
PDB Unreleased entry


Resolution: 3→50 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 5677 -RANDOM
Rwork0.24 ---
all0.279 113714 --
obs0.262 113171 99.9 %-
Displacement parametersBiso mean: 80 Å2
Baniso -1Baniso -2Baniso -3
1--13.51 Å20 Å20 Å2
2--22.367 Å20 Å2
3----8.857 Å2
Refinement stepCycle: LAST / Resolution: 3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31616 0 4 0 31620
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_deg1.38
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 DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2ION.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor Rfree: 0.28 / Rfactor Rwork: 0.24
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.35

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