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- PDB-6asr: REV1 UBM2 domain complex with ubiquitin -

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Basic information

Entry
Database: PDB / ID: 6asr
TitleREV1 UBM2 domain complex with ubiquitin
Components
  • DNA repair protein REV1
  • Ubiquitin
KeywordsPROTEIN BINDING / ubiquitin-binding motif / protein-protein interaction
Function / homology
Function and homology information


deoxycytidyl transferase activity / symbiont entry into host cell via disruption of host cell glycocalyx / error-free translesion synthesis / symbiont entry into host cell via disruption of host cell envelope / virus tail / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI ...deoxycytidyl transferase activity / symbiont entry into host cell via disruption of host cell glycocalyx / error-free translesion synthesis / symbiont entry into host cell via disruption of host cell envelope / virus tail / error-prone translesion synthesis / response to UV / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / damaged DNA binding / DNA-directed DNA polymerase activity / DNA replication / nucleoplasm / metal ion binding
Similarity search - Function
DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / Pectate lyase superfamily protein ...DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / DNA repair protein Rev1 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / : / DNA polymerase-iota, thumb domain / Pectate lyase superfamily protein / Rhamnogalacturonase A/epimerase, pectate lyase-like / BRCA1 C Terminus (BRCT) domain / DNA polymerase, Y-family, little finger domain / impB/mucB/samB family C-terminal domain / UmuC domain / DNA polymerase, Y-family, little finger domain superfamily / impB/mucB/samB family / UmuC domain profile. / breast cancer carboxy-terminal domain / Pectin lyase fold / Pectin lyase fold/virulence factor / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Ubiquitin family / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
NICKEL (II) ION / Tail fiber / DNA repair protein REV1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.356 Å
AuthorsMiller, D.J.
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structures of REV1 UBM2 Domain Complex with Ubiquitin and with a Small-Molecule that Inhibits the REV1 UBM2-Ubiquitin Interaction.
Authors: Vanarotti, M. / Grace, C.R. / Miller, D.J. / Actis, M.L. / Inoue, A. / Evison, B.J. / Vaithiyalingam, S. / Singh, A.P. / McDonald, E.T. / Fujii, N.
History
DepositionAug 25, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ubiquitin
B: DNA repair protein REV1
C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8097
Polymers22,5753
Non-polymers2354
Water1,31573
1
A: Ubiquitin
B: DNA repair protein REV1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1745
Polymers13,9982
Non-polymers1763
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1860 Å2
ΔGint-27 kcal/mol
Surface area6420 Å2
MethodPISA
2
B: DNA repair protein REV1
hetero molecules

C: Ubiquitin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1154
Polymers13,9982
Non-polymers1172
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555z,-x,-y1
Buried area1070 Å2
ΔGint-27 kcal/mol
Surface area7070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.924, 164.924, 164.924
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number211
Space group name H-MI432
Components on special symmetry positions
IDModelComponents
11B-1208-

HOH

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Components

#1: Protein Ubiquitin


Mass: 8576.831 Da / Num. of mol.: 2 / Fragment: residues 1-76
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: UBB / Production host: Escherichia coli (E. coli) / References: UniProt: P0CG47
#2: Protein DNA repair protein REV1 / Alpha integrin-binding protein 80 / AIBP80 / Rev1-like terminal deoxycytidyl transferase


Mass: 5420.993 Da / Num. of mol.: 1 / Fragment: residues 998-1040
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases
#3: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 1

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Sample preparation

CrystalDensity Matthews: 4.14 Å3/Da / Density % sol: 70.29 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6 / Details: 0.1 M MES pH 6.0, 10 % PEG 8000 / PH range: 6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 19, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 16003 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Rsym value: 0.106 / Net I/σ(I): 15.9
Reflection shellResolution: 2.35→2.39 Å / Redundancy: 5 % / Num. unique obs: 781 / Rsym value: 0.532 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4s1z

4s1z


Resolution: 2.356→28.284 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 863 5.39 %
Rwork0.2008 --
obs0.2025 16000 99.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.356→28.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1476 0 4 73 1553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061509
X-RAY DIFFRACTIONf_angle_d0.492014
X-RAY DIFFRACTIONf_dihedral_angle_d18.474936
X-RAY DIFFRACTIONf_chiral_restr0.043241
X-RAY DIFFRACTIONf_plane_restr0.004262
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3556-2.50310.2881380.25542496X-RAY DIFFRACTION100
2.5031-2.69620.2761240.23422518X-RAY DIFFRACTION100
2.6962-2.96730.23461430.22712502X-RAY DIFFRACTION100
2.9673-3.3960.2311340.2122524X-RAY DIFFRACTION100
3.396-4.27630.21821650.18542522X-RAY DIFFRACTION99
4.2763-28.28630.21321590.17552575X-RAY DIFFRACTION96

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