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- PDB-3gqc: Structure of human Rev1-DNA-dNTP ternary complex -

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Basic information

Entry
Database: PDB / ID: 3gqc
TitleStructure of human Rev1-DNA-dNTP ternary complex
Components
  • 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
  • 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
  • DNA repair protein REV1
KeywordsTRANSFERASE/DNA / PROTEIN-DNA COMPLEX / DNA damage / DNA repair / DNA synthesis / DNA-binding / Magnesium / Metal-binding / Nucleotidyltransferase / Nucleus / Transferase / TRANSFERASE-DNA COMPLEX
Function / homology
Function and homology information


deoxycytidyl transferase activity / error-free translesion synthesis / 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 / DNA replication ...deoxycytidyl transferase activity / error-free translesion synthesis / 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 / DNA replication / damaged DNA binding / DNA-directed DNA polymerase activity / 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 / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / DNA repair protein Rev1 / DNApol eta/Rev1, HhH motif / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 ...DNA repair protein Rev1, C-terminal / Rev1, C-terminal domain superfamily / : / DNA repair protein REV1 C-terminal domain / HUWE1/Rev1, ubiquitin binding region / Ubiquitin binding region / DNA repair protein Rev1 / DNApol eta/Rev1, HhH motif / DNA polymerase, Y-family, little finger domain / MutS, DNA mismatch repair protein, domain I - #60 / MutS, DNA mismatch repair protein, domain I / 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 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / Dna Ligase; domain 1 / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / Reverse transcriptase/Diguanylate cyclase domain / Alpha-Beta Plaits / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / DNA / DNA (> 10) / DNA repair protein REV1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSwan, M.K. / Aggarwal, A.K.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structure of the human Rev1-DNA-dNTP ternary complex.
Authors: Swan, M.K. / Johnson, R.E. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionMar 24, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 19, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Sep 6, 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 / 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_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_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.pdbx_leaving_atom_flag / _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.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_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: DNA repair protein REV1
B: DNA repair protein REV1
C: DNA repair protein REV1
D: DNA repair protein REV1
E: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
F: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
G: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
H: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
I: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
J: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
K: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
L: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)260,16729
Polymers257,98312
Non-polymers2,18517
Water1,72996
1
A: DNA repair protein REV1
E: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
F: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0608
Polymers64,4963
Non-polymers5645
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA repair protein REV1
G: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
H: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0116
Polymers64,4963
Non-polymers5163
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: DNA repair protein REV1
I: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
J: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0367
Polymers64,4963
Non-polymers5404
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: DNA repair protein REV1
K: 5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'
L: 5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,0608
Polymers64,4963
Non-polymers5645
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)56.436, 172.780, 129.192
Angle α, β, γ (deg.)90.00, 90.65, 90.00
Int Tables number4
Space group name H-MP1211
DetailsTHE BIOLOGICAL UNIT IS THE PROTEIN-DNA COMPLEX SINGLE PROTEIN CHAIN WITH 12/16 PRIMER/TEMPLATE DNA AND INCOMING DCTP

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
DNA repair protein REV1 / / Rev1-like terminal deoxycytidyl transferase / Alpha integrin-binding protein 80 / AIBP80


Mass: 55926.055 Da / Num. of mol.: 4 / Fragment: UNP residues 330-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REV1, REV1L / Plasmid: pTYB4SE110 / Production host: Escherichia coli (E. coli) / Strain (production host): ER2566
References: UniProt: Q9UBZ9, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

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DNA chain , 2 types, 8 molecules EGIKFHJL

#2: DNA chain
5'-D(*AP*TP*CP*CP*TP*CP*CP*CP*CP*TP*AP*(DOC))-3'


Mass: 3502.308 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic DNA
#3: DNA chain
5'-D(*TP*AP*AP*GP*GP*TP*AP*GP*GP*GP*GP*AP*GP*GP*AP*T)-3'


Mass: 5067.301 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Synthetic DNA

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Non-polymers , 3 types, 113 molecules

#4: Chemical
ChemComp-DCP / 2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE / Deoxycytidine triphosphate


Mass: 467.157 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C9H16N3O13P3
#5: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 96 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG MME 5000, 400mM Sodium malonate pH 4.6, 100mM Ammonium sulfate, 200mM Sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Components of the solutions
IDNameCrystal-IDSol-ID
1Water11
2Water12

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 28, 2006
Details: Cryogenically cooled double crystal monochromator with horizontal focusing sagitally bent second mono crystal with 4:1 magnification ratio and vertically focusing mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→43.07 Å / Num. obs: 72489 / % possible obs: 94.7 % / Redundancy: 3.3 % / Rsym value: 0.059 / Net I/σ(I): 27.4
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 3.1 % / Mean I/σ(I) obs: 2.9375 / Rsym value: 0.462 / % possible all: 91.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AQ4

2aq4


Resolution: 2.5→43.07 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.902 / SU B: 16.566 / SU ML: 0.232 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.689 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26709 8037 10 %RANDOM
Rwork0.21353 ---
obs0.2189 72489 94.39 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.853 Å2
Baniso -1Baniso -2Baniso -3
1--0.44 Å20 Å2-1.14 Å2
2--2.77 Å20 Å2
3----2.36 Å2
Refinement stepCycle: LAST / Resolution: 2.5→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13025 2276 125 96 15522
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02215925
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3432.14922039
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.32651717
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.87223.636550
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.682152197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4361591
X-RAY DIFFRACTIONr_chiral_restr0.0850.22497
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211183
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.26436
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3030.210605
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2526
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1530.2118
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5811.58786
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.998213680
X-RAY DIFFRACTIONr_scbond_it1.32138805
X-RAY DIFFRACTIONr_scangle_it2.1134.58359
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.402 555 -
Rwork0.326 5080 -
obs--88.96 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.19630.336-0.00831.2949-0.11790.5943-0.00470.0163-0.04550.00430.00470.03160.0306-0.03220-0.1176-0.01310.0102-0.14680.0063-0.1643-0.589-25.71699.3986
21.22320.03780.22811.648-0.09830.9807-0.0771-0.01470.0405-0.04720.10290.0604-0.0887-0.0932-0.0258-0.103-0.02930.0023-0.13290.027-0.094815.424220.288316.9756
32.53720.95540.38141.80020.08711.17090.1126-0.07170.22390.1951-0.00960.1795-0.191-0.1334-0.103-0.1576-0.01460.0359-0.1258-0.0094-0.134923.805953.029-50.6093
41.3042-0.05820.09181.0940.01481.1175-0.04750.0116-0.0141-0.0340.04860.01140.11630.0836-0.0011-0.0906-0.0171-0.0234-0.07220.0241-0.015614.16941.5911-47.7189
59.6593-3.23138.39883.5385-8.982122.80630.51070.99750.0696-0.1295-0.37950.10080.72331.4687-0.13120.00440.11230.07670.09210.00470.0935-8.6455-15.1348-4.0865
66.4797-1.39413.23490.9673-1.2683.8001-0.14220.57140.30990.00320.142-0.1037-0.2994-0.0370.0002-0.2284-0.0140.0318-0.1470.095-0.2134-2.0052-16.6629-1.2005
711.983-3.2621-7.0314.69099.09717.69280.1759-0.97540.8369-0.1760.9169-0.5471-0.25950.7193-1.0928-0.0029-0.0760.05070.0261-0.038-0.0297.014724.06733.6392
87.4016-3.0255-4.00451.72012.28974.0075-0.4024-0.52070.19010.3160.1426-0.13510.2929-0.10620.2598-0.0748-0.0040.0129-0.0283-0.1098-0.094913.673422.655630.7035
99.4782-0.3995-4.53532.27286.108318.57450.14371.2295-0.6466-0.4533-0.3116-0.198-0.5589-0.83970.16790.06830.1268-0.08070.0517-0.06950.077939.252137.083-68.8133
105.8904-1.1392-1.62461.44861.18182.63850.09020.8056-0.3712-0.22950.0728-0.21720.50020.0122-0.1630.0548-0.0227-0.05590.1313-0.03630.022132.564138.5234-65.9119
1111.2761-3.21676.27258.5342-12.28118.10750.2449-0.9151-0.8119-0.36430.74960.80330.3684-0.3473-0.99450.0284-0.0759-0.02760.01560.02520.037922.2979-2.1791-30.9729
127.1641-2.13253.50531.5673-1.43914.225-0.2309-0.7954-0.19780.25450.2370.1756-0.2244-0.0714-0.0061-0.16090.0080.0472-0.03190.1199-0.045715.7215-0.7608-33.9025
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A348 - 375
2X-RAY DIFFRACTION1A417 - 463
3X-RAY DIFFRACTION1A502 - 825
4X-RAY DIFFRACTION2B348 - 375
5X-RAY DIFFRACTION2B417 - 463
6X-RAY DIFFRACTION2B502 - 825
7X-RAY DIFFRACTION3C348 - 375
8X-RAY DIFFRACTION3C417 - 463
9X-RAY DIFFRACTION4D348 - 375
10X-RAY DIFFRACTION4D417 - 463
11X-RAY DIFFRACTION4D502 - 825
12X-RAY DIFFRACTION5E1 - 12
13X-RAY DIFFRACTION6F1 - 16
14X-RAY DIFFRACTION7G1 - 12
15X-RAY DIFFRACTION8H1 - 16
16X-RAY DIFFRACTION9I1 - 12
17X-RAY DIFFRACTION10J1 - 16
18X-RAY DIFFRACTION11K1 - 12
19X-RAY DIFFRACTION12L1 - 16

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