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- PDB-5vzb: Post-catalytic complex of human Polymerase Mu (G433S) mutant with... -

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Basic information

Entry
Database: PDB / ID: 5vzb
TitlePost-catalytic complex of human Polymerase Mu (G433S) mutant with incoming UTP
Components
  • DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA-directed DNA/RNA polymerase mu
  • DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3')
KeywordsTRANSFERASE/DNA / Family X / nonhomologous end-joining / DNA double strand break repair / ribonucleotide incorporation / TRANSFERASE-DNA complex
Function / homology
Function and homology information


Nonhomologous End-Joining (NHEJ) / double-strand break repair via nonhomologous end joining / DNA recombination / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X ...DNA-directed DNA/RNA polymerase mu / DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu / Beta Polymerase; domain 3 / DNA polymerase, thumb domain / DNA polymerase beta, N-terminal domain-like / DNA polymerase beta, palm domain / DNA polymerase beta palm / DNA polymerase lambda, fingers domain / Fingers domain of DNA polymerase lambda / DNA-directed DNA polymerase X / DNA polymerase beta-like, N-terminal domain / Helix-hairpin-helix domain / DNA polymerase X family / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X, binding site / DNA polymerase family X signature. / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase beta thumb / DNA polymerase, thumb domain superfamily / Beta Polymerase, domain 2 / Beta Polymerase; domain 2 / BRCT domain profile. / BRCT domain / BRCT domain superfamily / Nucleotidyltransferase superfamily / 5' to 3' exonuclease, C-terminal subdomain / DNA polymerase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
URIDINE 5'-TRIPHOSPHATE / DNA / DNA/RNA hybrid / DNA-directed DNA/RNA polymerase mu
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMoon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES 102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
American Cancer SocietyPF-14-0438-01-DMC United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA097096 United States
CitationJournal: Nucleic Acids Res. / Year: 2017
Title: Structural accommodation of ribonucleotide incorporation by the DNA repair enzyme polymerase Mu.
Authors: Moon, A.F. / Pryor, J.M. / Ramsden, D.A. / Kunkel, T.A. / Bebenek, K. / Pedersen, L.C.
History
DepositionMay 27, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 5, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Sep 27, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Dec 4, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 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_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA-directed DNA/RNA polymerase mu
T: DNA (5'-D(*CP*GP*GP*CP*AP*TP*AP*CP*G)-3')
P: DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3')
D: DNA (5'-D(P*GP*CP*CP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,07913
Polymers45,3044
Non-polymers7759
Water6,810378
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.807, 68.843, 109.848
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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DNA chain , 2 types, 2 molecules TD

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


Mass: 2740.812 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(P*GP*CP*CP*G)-3')


Mass: 1191.818 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / DNA/RNA hybrid , 2 types, 2 molecules AP

#1: Protein DNA-directed DNA/RNA polymerase mu / Pol Mu / Terminal transferase


Mass: 39874.188 Da / Num. of mol.: 1 / Fragment: residues 134-494 / Mutation: G433S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLM, polmu / Plasmid: pGEXM / Production host: Escherichia coli (E. coli) / References: UniProt: Q9NP87, DNA-directed DNA polymerase
#3: DNA/RNA hybrid DNA/RNA (5'-D(*CP*GP*TP*A)-R(P*U)-3')


Mass: 1496.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 6 types, 387 molecules

#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-UTP / URIDINE 5'-TRIPHOSPHATE / Uridine triphosphate


Mass: 484.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H15N2O15P3 / Comment: UTP*YM
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 378 / 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: 2.5 Å3/Da / Density % sol: 50.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 90mM HEPES pH 7.5, 18% PEG4K

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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: Apr 13, 2017 / Details: Rosenbaum-Rock vertical focusing mirror
RadiationMonochromator: Rosenbaum-Rock monochromator high-resolution double-crystal Si(220) sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 72904 / % possible obs: 99.5 % / Redundancy: 6.8 % / Rpim(I) all: 0.027 / Rsym value: 0.065 / Χ2: 0.933 / Net I/σ(I): 25.34
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.45 / Num. unique obs: 3437 / CC1/2: 0.688 / Rpim(I) all: 0.339 / Rsym value: 0.578 / Χ2: 0.836 / % possible all: 95.8

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4M04
Resolution: 1.5→32.328 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.49 / Phase error: 17.2
Details: THE AUTHORS STATE THAT THE ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT THE METAL OCCUPYING THE HHH2 SITE (PEAK > 10 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ADDED, ...Details: THE AUTHORS STATE THAT THE ANOMALOUS SIGNAL IS OBSERVED AT ONE POSITION IN THIS STRUCTURE--AT THE METAL OCCUPYING THE HHH2 SITE (PEAK > 10 SIGMA). NO KNOWN ANOMALOUS SCATTERERS WERE ADDED, SO THIS POSITION HAS BEEN PUTATIVELY MODELED AS SODIUM, WHICH IS CONSISTENT WITH ITS IDENTITY IN OTHER REPORTED STRUCTURES.
RfactorNum. reflection% reflectionSelection details
Rfree0.1874 3569 5.01 %random
Rwork0.1707 ---
obs0.1716 71285 97.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.5→32.328 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2534 349 43 378 3304
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093267
X-RAY DIFFRACTIONf_angle_d1.0754554
X-RAY DIFFRACTIONf_dihedral_angle_d12.5291047
X-RAY DIFFRACTIONf_chiral_restr0.074504
X-RAY DIFFRACTIONf_plane_restr0.007531
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.499-1.51950.2427950.22581754X-RAY DIFFRACTION64
1.5195-1.54130.25111120.22092287X-RAY DIFFRACTION83
1.5413-1.56430.2361380.19992519X-RAY DIFFRACTION91
1.5643-1.58870.19331400.18332633X-RAY DIFFRACTION96
1.5887-1.61470.19431440.17572704X-RAY DIFFRACTION98
1.6147-1.64260.18571450.16582749X-RAY DIFFRACTION99
1.6426-1.67250.19251440.16592729X-RAY DIFFRACTION100
1.6725-1.70460.19041450.16542772X-RAY DIFFRACTION100
1.7046-1.73940.17021460.15832765X-RAY DIFFRACTION100
1.7394-1.77720.17031450.16352764X-RAY DIFFRACTION100
1.7772-1.81860.17251460.16542778X-RAY DIFFRACTION100
1.8186-1.8640.20151470.16962775X-RAY DIFFRACTION100
1.864-1.91440.19241450.16452765X-RAY DIFFRACTION100
1.9144-1.97080.20491470.17062761X-RAY DIFFRACTION100
1.9708-2.03440.19381430.16312790X-RAY DIFFRACTION100
2.0344-2.10710.17271460.16722773X-RAY DIFFRACTION100
2.1071-2.19140.16361460.16682799X-RAY DIFFRACTION100
2.1914-2.29110.1911510.16712788X-RAY DIFFRACTION100
2.2911-2.41190.17741450.16962792X-RAY DIFFRACTION100
2.4119-2.56290.20581510.17952801X-RAY DIFFRACTION100
2.5629-2.76070.21071480.18332824X-RAY DIFFRACTION100
2.7607-3.03830.21411490.18742822X-RAY DIFFRACTION100
3.0383-3.47760.19061480.16892830X-RAY DIFFRACTION100
3.4776-4.37960.13241510.14812877X-RAY DIFFRACTION100
4.3796-32.33530.20451520.17842865X-RAY DIFFRACTION95
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
11.0188-0.39040.16191.0454-0.22511.32090.05680.2068-0.1505-0.1012-0.1043-0.12310.18240.270.05590.11090.0493-0.00180.1307-0.03040.111612.9183-18.5598-14.5991
20.693-0.2783-0.32070.970.69111.33160.11730.23050.2501-0.3476-0.0471-0.3623-0.31690.1215-0.03780.1618-0.00450.07910.18090.0550.237917.07768.138-16.9489
31.4144-0.1564-0.1661.36120.08880.56710.0907-0.11830.37170.1098-0.067-0.0765-0.1026-0.02580.00660.0796-0.00590.01850.0631-0.01870.1134-2.08218.7632-0.7048
41.1995-0.1213-0.39771.33680.19950.97040.06020.3263-0.1776-0.121-0.08430.18850.0309-0.1823-0.00390.05790.0067-0.01420.0905-0.02320.0604-10.8904-10.3202-11.2188
50.3107-0.0615-0.08150.69970.15140.30180.0860.3219-0.0622-0.2886-0.05440.0489-0.0012-0.05370.00820.16550.0281-0.01960.2108-0.03490.0660.5885-8.7347-23.3143
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 138:231
2X-RAY DIFFRACTION2chain A and resid 232:289
3X-RAY DIFFRACTION3chain A and resid 290:423
4X-RAY DIFFRACTION4chain A and resid 424:494
5X-RAY DIFFRACTION5chain T or chain P or chain D

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