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- PDB-1yov: Insights into the Ubiquitin Transfer Cascade from the refined str... -

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Basic information

Entry
Database: PDB / ID: 1yov
TitleInsights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8
Components
  • Amyloid protein-binding protein 1
  • Ubiquitin-activating enzyme E1C
KeywordsSIGNALING PROTEIN / ubiquitin / NEDD8 / E1 / APPBP1 / UBA3
Function / homology
Function and homology information


E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / mitotic DNA replication checkpoint signaling / protein neddylation / regulation of neuron apoptotic process / post-translational protein modification / NIK-->noncanonical NF-kB signaling ...E1 NEDD8-activating enzyme / NEDD8 activating enzyme activity / endomitotic cell cycle / ubiquitin activating enzyme activity / NEDD8 transferase activity / mitotic DNA replication checkpoint signaling / protein neddylation / regulation of neuron apoptotic process / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / Antigen processing: Ubiquitination & Proteasome degradation / 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 / signal transduction / protein-containing complex / proteolysis / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm
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 / Ubiquitin-activating enzyme E1, Cys active site / Ubiquitin-activating enzyme 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 / 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 / Ubiquitin-like (UB roll) / Arc Repressor Mutant, subunit A / NAD(P)-binding Rossmann-like Domain / Roll / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
NEDD8-activating enzyme E1 regulatory subunit / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsWalden, H. / Podgorski, M.S. / Schulman, B.A.
CitationJournal: Nature / Year: 2003
Title: Insights into the Ubiquitin Transfer Cascade from the refined structure of the activating enzyme for NEDD8
Authors: Walden, H. / Podgorski, M.S. / Schulman, B.A.
History
DepositionJan 28, 2005Deposition site: RCSB / Processing site: RCSB
SupersessionMar 8, 2005ID: 1NGV
Revision 1.0Mar 8, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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.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_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Amyloid protein-binding protein 1
B: Ubiquitin-activating enzyme E1C
C: Amyloid protein-binding protein 1
D: Ubiquitin-activating enzyme E1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,5776
Polymers220,4464
Non-polymers1312
Water2,702150
1
A: Amyloid protein-binding protein 1
B: Ubiquitin-activating enzyme E1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2883
Polymers110,2232
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-29 kcal/mol
Surface area38660 Å2
MethodPISA
2
C: Amyloid protein-binding protein 1
D: Ubiquitin-activating enzyme E1C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2883
Polymers110,2232
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6390 Å2
ΔGint-24 kcal/mol
Surface area39290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.400, 123.600, 198.200
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 protein-binding protein 1 / / Amyloid beta precursor protein-binding protein 1 / 59 kDa / APP-BP1 / Protooncogene protein 1 / HPP1


Mass: 60688.641 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: APPBP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13564
#2: Protein Ubiquitin-activating enzyme E1C / Nedd8-activating enzyme E1C / Ubiquitin-activating enzyme 3 homolog


Mass: 49534.441 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE1C, UBA3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8TBC4
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PME5500, HEPES, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDCrystal-ID
11
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 5.0.211.15
SYNCHROTRONNSLS X2520.9799, 0.98, 0.95
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
11.151
20.97991
30.981
40.951
ReflectionResolution: 2.6→10 Å / Num. all: 70374 / Num. obs: 67993 / % possible obs: 96.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2
Reflection shellResolution: 2.6→2.69 Å / % possible all: 95.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
RefinementMethod to determine structure: MAD / Resolution: 2.6→10 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: According to authors: This is a correction of the misaligned 2 C-terminal strands, and data is published according to 1Y8X
RfactorNum. reflectionSelection details
Rfree0.28 3445 random
Rwork0.236 --
all-70374 -
obs-67993 -
Refinement stepCycle: LAST / Resolution: 2.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14452 0 2 150 14604

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