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- PDB-7pyv: Crystal structure of human UBA6 in complex with the ubiquitin-lik... -

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Basic information

Entry
Database: PDB / ID: 7pyv
TitleCrystal structure of human UBA6 in complex with the ubiquitin-like modifier FAT10
Components
  • UBD
  • Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6
KeywordsHYDROLASE / ubiquitin activating enzyme UBA6 / human leukocyte antigen (HLA)-F adjacent transcript 10(FAT10) / FAT10ylation / post-translational modification / ubiquitin-like modifier
Function / homology
Function and homology information


FAT10 activating enzyme activity / amygdala development / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / thiosulfate sulfurtransferase activity / dendritic spine development / proteasome binding / response to tumor necrosis factor / nucleotidyltransferase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes ...FAT10 activating enzyme activity / amygdala development / E1 ubiquitin-activating enzyme / ubiquitin activating enzyme activity / thiosulfate sulfurtransferase activity / dendritic spine development / proteasome binding / response to tumor necrosis factor / nucleotidyltransferase activity / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / learning / locomotory behavior / hippocampus development / Antigen processing: Ubiquitination & Proteasome degradation / ubiquitin-dependent protein catabolic process / protein ubiquitination / DNA damage response / mitochondrion / RNA binding / extracellular exosome / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
Similarity search - Function
Ubiquitin D / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily ...Ubiquitin D / Ubiquitin-activating enzyme E1, conserved site / Ubiquitin-activating enzyme signature 1. / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme E1, C-terminal / Ubiquitin-activating enzyme E1, FCCH domain / Ubiquitin-activating enzyme E1, four-helix bundle / Ubiquitin-activating enzyme E1, C-terminal domain superfamily / Ubiquitin-activating enzyme E1, SCCH domain / Ubiquitin-activating enzyme E1, FCCH domain superfamily / Ubiquitin fold domain / Ubiquitin-activating enzyme E1 FCCH domain / Ubiquitin-activating enzyme E1 four-helix bundle / Ubiquitin-activating enzyme e1 C-terminal domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin-activating enzyme, SCCH domain / Ubiquitin/SUMO-activating enzyme E1-like / Ubiquitin-activating enzyme E1, inactive adenylation domain, subdomain 1 / 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 domain / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
UBD / Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-like modifier-activating enzyme 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.27 Å
AuthorsLi, S. / Truongvan, N. / Schindelin, H.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)2243 Germany
CitationJournal: Nat Commun / Year: 2022
Title: Structures of UBA6 explain its dual specificity for ubiquitin and FAT10.
Authors: Truongvan, N. / Li, S. / Misra, M. / Kuhn, M. / Schindelin, H.
History
DepositionOct 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 24, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6
C: UBD
B: Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6


Theoretical massNumber of molelcules
Total (without water)251,3803
Polymers251,3803
Non-polymers00
Water00
1
A: Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6
C: UBD


Theoretical massNumber of molelcules
Total (without water)134,6422
Polymers134,6422
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3450 Å2
ΔGint-9 kcal/mol
Surface area52340 Å2
MethodPISA
2
B: Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6


Theoretical massNumber of molelcules
Total (without water)116,7381
Polymers116,7381
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area45710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.458, 93.593, 109.542
Angle α, β, γ (deg.)70.519, 88.537, 74.593
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

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Components

#1: Protein Ubiquitin-like modifier-activating enzyme 6,Ubiquitin-like modifier-activating enzyme 1,Ubiquitin-like modifier-activating enzyme 6 / Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like ...Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like protein 2 / E1-L2 / Protein A1S9 / Ubiquitin-activating enzyme E1 / Ubiquitin-activating enzyme 6 / Monocyte protein 4 / MOP-4 / Ubiquitin-activating enzyme E1-like protein 2 / E1-L2


Mass: 116737.570 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBA6, MOP4, UBE1L2, UBA1, A1S9T, UBE1 / Production host: Escherichia coli (E. coli)
References: UniProt: A0AVT1, UniProt: P22314, E1 ubiquitin-activating enzyme
#2: Protein UBD


Mass: 17904.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1U9X8S9

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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: 3.56 Å3/Da / Density % sol: 65.5 % / Description: Plates
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8.4
Details: 0.5 M Lithium chloride, 0.1 M Tris pH 8.4, 25% PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Jul 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3.268→46.093 Å / Num. obs: 30812 / % possible obs: 59.07 % / Redundancy: 3.84 % / Biso Wilson estimate: 90.24 Å2 / CC1/2: 0.9881 / Rmerge(I) obs: 0.202 / Rpim(I) all: 0.12 / Rrim(I) all: 0.236 / Net I/σ(I): 5.2
Reflection shellResolution: 3.268→3.705 Å / Redundancy: 3.9 % / Rmerge(I) obs: 1.092 / Num. unique obs: 1542 / CC1/2: 0.401 / Rpim(I) all: 0.64 / Rrim(I) all: 1.266 / % possible all: 53.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PVN, 6GF1, 6GF2

7pvn

6gf1

6gf2


Resolution: 3.27→45.14 Å / SU ML: 0.362 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 29.0477 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2392 875 2.84 %
Rwork0.2159 29918 -
obs0.2166 30793 59.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 111.34 Å2
Refinement stepCycle: LAST / Resolution: 3.27→45.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16503 0 0 0 16503
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004716883
X-RAY DIFFRACTIONf_angle_d0.757322929
X-RAY DIFFRACTIONf_chiral_restr0.04392610
X-RAY DIFFRACTIONf_plane_restr0.00762954
X-RAY DIFFRACTIONf_dihedral_angle_d17.322910201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.27-3.470.301470.3214260X-RAY DIFFRACTION3.06
3.47-3.740.3658510.30071535X-RAY DIFFRACTION18.34
3.74-4.120.29311380.26594775X-RAY DIFFRACTION56.81
4.12-4.710.26322140.22457426X-RAY DIFFRACTION87.72
4.71-5.930.25222220.22317577X-RAY DIFFRACTION89.85
5.93-45.140.19612430.18748345X-RAY DIFFRACTION98.86

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