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- PDB-3dbr: Structural Dissection of a Gating Mechanism Preventing Misactivat... -

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Basic information

Entry
Database: PDB / ID: 3dbr
TitleStructural Dissection of a Gating Mechanism Preventing Misactivation of Ubiquitin by NEDD8's E1 (APPBP1-UBA3Arg190Gln-NEDD8Ala72Arg)
Components
  • NEDD8-activating enzyme E1 catalytic subunit
  • NEDD8-activating enzyme E1 regulatory subunit
  • NEDD8
KeywordsCELL CYCLE / activating enzyme / Apoptosis / Membrane / Ubl conjugation pathway / ATP-binding / Ligase / Nucleotide-binding / Polymorphism / Nucleus
Function / homology
Function and homology information


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 ...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 / UCH proteinases / 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, 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 / Ubiquitin-activating enzyme / THIF-type NAD/FAD binding fold / ThiF family / Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 / Ubiquitin conserved site / Ubiquitin domain / Ubiquitin domain signature. / 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
NEDD8-activating enzyme E1 regulatory subunit / NEDD8 / NEDD8-activating enzyme E1 catalytic subunit
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / rigid body refinement / Resolution: 3.05 Å
AuthorsSouphron, J. / Schulman, B.A.
CitationJournal: Biochemistry / Year: 2008
Title: Structural dissection of a gating mechanism preventing misactivation of ubiquitin by NEDD8's E1.
Authors: Souphron, J. / Waddell, M.B. / Paydar, A. / Tokgoz-Gromley, Z. / Roussel, M.F. / Schulman, B.A.
History
DepositionJun 2, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / 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 / _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
Revision 1.3Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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: NEDD8-activating enzyme E1 catalytic subunit
I: NEDD8
C: NEDD8-activating enzyme E1 regulatory subunit
D: NEDD8-activating enzyme E1 catalytic subunit
J: NEDD8
E: NEDD8-activating enzyme E1 regulatory subunit
F: NEDD8-activating enzyme E1 catalytic subunit
K: NEDD8
G: NEDD8-activating enzyme E1 regulatory subunit
H: NEDD8-activating enzyme E1 catalytic subunit
L: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)473,99616
Polymers473,73512
Non-polymers2624
Water0
1
E: NEDD8-activating enzyme E1 regulatory subunit
F: NEDD8-activating enzyme E1 catalytic subunit
K: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4994
Polymers118,4343
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-34 kcal/mol
Surface area42050 Å2
MethodPISA
2
G: NEDD8-activating enzyme E1 regulatory subunit
H: NEDD8-activating enzyme E1 catalytic subunit
L: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4994
Polymers118,4343
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-31 kcal/mol
Surface area41160 Å2
MethodPISA
3
C: NEDD8-activating enzyme E1 regulatory subunit
D: NEDD8-activating enzyme E1 catalytic subunit
J: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4994
Polymers118,4343
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10590 Å2
ΔGint-34 kcal/mol
Surface area41380 Å2
MethodPISA
4
A: NEDD8-activating enzyme E1 regulatory subunit
B: NEDD8-activating enzyme E1 catalytic subunit
I: NEDD8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,4994
Polymers118,4343
Non-polymers651
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10370 Å2
ΔGint-30 kcal/mol
Surface area42290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)134.322, 198.531, 208.795
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
NEDD8-activating enzyme E1 regulatory subunit / Amyloid protein-binding protein 1 / Amyloid beta protein-binding protein 1 / 59 kDa / APP-BP1 / ...Amyloid protein-binding protein 1 / Amyloid beta protein-binding protein 1 / 59 kDa / APP-BP1 / Proto-oncogene protein 1


Mass: 59973.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NAE1, APPBP1 / Plasmid: pABLO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold (DE3) / References: UniProt: Q13564
#2: Protein
NEDD8-activating enzyme E1 catalytic subunit / Ubiquitin- like modifier-activating enzyme 3 / Ubiquitin-activating enzyme 3 / NEDD8-activating ...Ubiquitin- like modifier-activating enzyme 3 / Ubiquitin-activating enzyme 3 / NEDD8-activating enzyme E1C / Ubiquitin-activating enzyme E1C


Mass: 48738.684 Da / Num. of mol.: 4 / Fragment: unp residues 33-463 / Mutation: R190Q, C216A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA3, UBE1C / Plasmid: pABLO / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold (DE3)
References: UniProt: Q8TBC4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#3: Protein
NEDD8 / / Ubiquitin-like protein Nedd8 / Neddylin


Mass: 9721.208 Da / Num. of mol.: 4 / Mutation: A172R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NEDD8 / Plasmid: pGEX2TK / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (RIL) / References: UniProt: Q15843
#4: Chemical
ChemComp-ZN / ZINC ION


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

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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: 2.94 Å3/Da / Density % sol: 58.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, 0.2 M NaCl, 10% PEG 10K, 8% PEG400, 5 mM DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 3.05→50 Å / Num. all: 100137 / Num. obs: 100052 / % possible obs: 95.9 % / Redundancy: 3.2 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 12.3
Reflection shellResolution: 3.05→3.36 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.7 / Num. unique all: 25073 / % possible all: 97.2

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Processing

Software
NameClassification
HKL-2000data collection
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: rigid body refinement
Starting model: PDB entry 3DBH

3dbh


Resolution: 3.05→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.28 5064 -random
Rwork0.23 ---
all-100137 --
obs-100052 93.7 %-
Displacement parametersBiso mean: 47.6 Å2
Baniso -1Baniso -2Baniso -3
1-21.794 Å2--
2---23.304 Å2-
3---1.51 Å2
Refinement stepCycle: LAST / Resolution: 3.05→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms32420 0 4 0 32424
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.59
X-RAY DIFFRACTIONc_bond_d0.009

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