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- PDB-1tt5: Structure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction req... -

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Basic information

Entry
Database: PDB / ID: 1tt5
TitleStructure of APPBP1-UBA3-Ubc12N26: a unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8
Components
  • Ubiquitin-conjugating enzyme E2 M
  • amyloid protein-binding protein 1
  • ubiquitin-activating enzyme E1C isoform 1
KeywordsCELL CYCLE / LIGASE
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 / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs ...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 / mitotic DNA replication checkpoint signaling / protein neddylation / TGF-beta receptor signaling activates SMADs / regulation of neuron apoptotic process / post-translational protein modification / NIK-->noncanonical NF-kB signaling / Dectin-1 mediated noncanonical NF-kB signaling / protein modification process / ubiquitin-protein transferase activity / positive regulation of neuron apoptotic 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 / nucleoplasm / 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-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 / 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-conjugating enzyme Ubc12 / NEDD8-activating enzyme E1 regulatory subunit / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHuang, D.T. / Miller, D.W. / Mathew, R. / Cassell, R. / Holton, J.M. / Roussel, M.F. / Schulman, B.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2004
Title: A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8.
Authors: Huang, D.T. / Miller, D.W. / Mathew, R. / Cassell, R. / Holton, J.M. / Roussel, M.F. / Schulman, B.A.
History
DepositionJun 21, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 14, 2004Provider: 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
Remark 999SEQUENCE Residue B SER 608 and Residue B VAL 701 are not linked. Distance of C-N bond is 6.15. ...SEQUENCE Residue B SER 608 and Residue B VAL 701 are not linked. Distance of C-N bond is 6.15. Residue B THR 384 and Residue B ASN 601 are linked together. The residues 600-1008 of chains B and D were modelled as alanines due to poor electron density. The residue names were assigned arbitrarily as there are multiple possible sequences consistent with the density, and the connectivity is unclear.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: amyloid protein-binding protein 1
B: ubiquitin-activating enzyme E1C isoform 1
C: amyloid protein-binding protein 1
D: ubiquitin-activating enzyme E1C isoform 1
E: Ubiquitin-conjugating enzyme E2 M
F: Ubiquitin-conjugating enzyme E2 M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)223,4298
Polymers223,2986
Non-polymers1312
Water5,368298
1
A: amyloid protein-binding protein 1
B: ubiquitin-activating enzyme E1C isoform 1
E: Ubiquitin-conjugating enzyme E2 M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7144
Polymers111,6493
Non-polymers651
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8730 Å2
ΔGint-39 kcal/mol
Surface area39620 Å2
MethodPISA
2
C: amyloid protein-binding protein 1
D: ubiquitin-activating enzyme E1C isoform 1
F: Ubiquitin-conjugating enzyme E2 M
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,7144
Polymers111,6493
Non-polymers651
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7800 Å2
ΔGint-32 kcal/mol
Surface area38630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.410, 122.770, 195.910
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 / / APPBP1


Mass: 59973.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 4502169, UniProt: Q13564*PLUS
#2: Protein ubiquitin-activating enzyme E1C isoform 1 / UBA3 / Nedd8-activating enzyme hUba3


Mass: 48799.812 Da / Num. of mol.: 2 / Fragment: residues 33-463
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 38045942, UniProt: Q8TBC4*PLUS
#3: Protein/peptide Ubiquitin-conjugating enzyme E2 M / UBC12N26 / Ubiquitin-protein ligase M / Ubiquitin carrier protein M / Nedd8-conjugating enzyme Ubc12


Mass: 2875.364 Da / Num. of mol.: 2 / Fragment: residues 1-26
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBE2M, UBC12 / Plasmid: pGEX4T3 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P61081
#4: Chemical ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 298 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.57 %

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Data collection

Diffraction
IDCrystal-ID
11
21
31
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONAPS 19-ID1
SYNCHROTRONALS 8.3.12
SYNCHROTRONNSLS X253
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.6→18 Å / Num. obs: 67222

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Processing

SoftwareName: CNS / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→18 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.279 3377 random
Rwork0.237 --
all-69023 -
obs-67217 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-9.555 Å20 Å20 Å2
2--3.503 Å20 Å2
3----13.059 Å2
Refinement stepCycle: LAST / Resolution: 2.6→18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14337 0 2 298 14637
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param

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