[English] 日本語
Yorodumi
- PDB-7m0c: Post-catalytic nicked complex of DNA Polymerase Lambda with bound... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7m0c
TitlePost-catalytic nicked complex of DNA Polymerase Lambda with bound mismatched DSB substrate
Components
  • DNA (5'-D(*CP*AP*GP*TP*GP*CP*T)-3')
  • DNA (5'-D(*CP*GP*GP*CP*AP*G)-3')
  • DNA (5'-D(*TP*AP*CP*TP*G)-3')
  • DNA (5'-D(P*GP*CP*CP*G)-3')
  • DNA polymerase lambda
KeywordsTRANSFERASE / Nonhomologous end-joining / Base Excision Repair
Function / homology
Function and homology information


DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break ...DNA biosynthetic process / Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases / 5'-deoxyribose-5-phosphate lyase activity / somatic hypermutation of immunoglobulin genes / base-excision repair, gap-filling / nucleotide-excision repair / Nonhomologous End-Joining (NHEJ) / double-strand break repair via homologous recombination / double-strand break repair via nonhomologous end joining / site of double-strand break / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / DNA replication / DNA binding / nucleoplasm / metal ion binding / nucleus
Similarity search - Function
DNA polymerase family X, beta-like / 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 family X, beta-like / 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 family X, binding site / DNA polymerase family X signature. / DNA polymerase lambda lyase domain superfamily / DNA polymerase family X / DNA polymerase beta, thumb domain / DNA polymerase, thumb domain superfamily / DNA polymerase beta thumb / 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
PYROPHOSPHATE / DNA / DNA polymerase lambda
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsKaminski, A.M. / Bebenek, K. / Pedersen, L.C. / Kunkel, T.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)1ZIA ES102645 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)Z01 ES065070 United States
CitationJournal: Not Published
Title: Comprehensive structural survey of DNA double-strand break synapsis by DNA Polymerase Lambda
Authors: Kaminski, A.M. / Bebenek, K. / Kunkel, T.A. / Pedersen, L.C.
History
DepositionMar 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / pdbx_initial_refinement_model
Item: _citation.journal_abbrev

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

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


Theoretical massNumber of molelcules
Total (without water)45,68714
Polymers45,1855
Non-polymers5029
Water1,946108
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6340 Å2
ΔGint-107 kcal/mol
Surface area17040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.205, 60.023, 139.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

-
Components

-
Protein , 1 types, 1 molecules A

#1: Protein DNA polymerase lambda / Pol Lambda / DNA polymerase beta-2 / Pol beta2 / DNA polymerase kappa


Mass: 38550.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: POLL / Plasmid: pGEXM / Production host: Escherichia coli (E. coli)
References: UniProt: Q9UGP5, DNA-directed DNA polymerase, Lyases; Carbon-oxygen lyases; Other carbon-oxygen lyases

-
DNA chain , 4 types, 4 molecules TUPD

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


Mass: 1834.230 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*AP*CP*TP*G)-3')


Mass: 1495.023 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: DNA chain DNA (5'-D(*CP*AP*GP*TP*GP*CP*T)-3')


Mass: 2113.410 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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)

-
Non-polymers , 7 types, 117 molecules

#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-PPV / PYROPHOSPHATE


Mass: 177.975 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H4O7P2
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#11: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 108 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 76.5mM Na cacodylate pH 6.5, 0.153M ammonium sulfate, 22.95% (w/v) PEG 8000, 13.5% (v/v) glycerol, 0.2M NDSB-201

-
Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.65→50 Å / Num. obs: 14351 / % possible obs: 99.7 % / Redundancy: 6.3 % / Biso Wilson estimate: 29.9 Å2 / CC1/2: 0.967 / CC star: 0.992 / Rsym value: 0.182 / Χ2: 0.698 / Net I/σ(I): 8.86
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 5.9 % / Mean I/σ(I) obs: 1.63 / Num. unique obs: 694 / CC1/2: 0.629 / CC star: 0.879 / Rsym value: 0.77 / Χ2: 0.464 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
PHENIX1.19_4092refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PFO

2pfo


Resolution: 2.65→39.37 Å / SU ML: 0.2549 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 21.5826
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 715 5 %random
Rwork0.1804 13587 --
obs0.1829 14302 99.2 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.27 Å2
Refinement stepCycle: LAST / Resolution: 2.65→39.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2525 444 24 108 3101
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00473111
X-RAY DIFFRACTIONf_angle_d0.68744307
X-RAY DIFFRACTIONf_chiral_restr0.0405477
X-RAY DIFFRACTIONf_plane_restr0.0033481
X-RAY DIFFRACTIONf_dihedral_angle_d13.3452942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.850.29051340.23852611X-RAY DIFFRACTION97.17
2.85-3.140.26711410.20772686X-RAY DIFFRACTION99.75
3.14-3.590.28231480.18372694X-RAY DIFFRACTION99.93
3.59-4.520.19821420.14882728X-RAY DIFFRACTION99.65
4.52-39.370.18151500.17352868X-RAY DIFFRACTION99.47
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)
10.453858260046-0.3310333001140.1040023401180.405410404352-0.1380725325680.2157169830690.08924187374320.11087410357-0.0227492138242-0.2513451975320.0317331115876-0.0720227193583-0.2046932937190.03547848939120.0396964805450.238882259913-0.03440569271290.06205020571370.17652850663-0.004285037495480.195198962668-7.7107750945525.4398069346-26.606625065
20.119140323221-0.0458612950861-0.1404184399230.3311878788130.1700280569960.248120745064-0.159785129496-0.1124971297520.02780322134410.18108493810.207877812510.006074020351930.0124163736526-0.1101434225460.006218090529330.1481218726670.000747202431282-0.002277117504430.159395947337-0.004304234264410.148003747656-13.634152941119.82169398860.902400861525
30.244224620351-0.03145769253370.01105698136720.5278692036220.185715573310.5883801794410.0460405802567-0.0206484906971-0.0355480658737-0.001621416732820.05875258369130.03644416706670.08734014284610.01157454759120.004102148317140.068070109411-0.0134113304519-0.004655788156620.0874602071640.0009749679688170.120346594851-12.1669946794-5.33386122389-7.43995536437
40.07165834997610.1033150058420.2450793190880.2169797628260.1062020481390.33929656601-0.0313004719095-0.05687972765320.0334450639566-0.2596270439140.06778556386340.04634616489540.0297560273401-0.05274790498390.004526755997560.1987853531490.0124135346142-0.02892792474910.112387265992-0.03120342765140.139725656592-20.01981598751.83165932557-27.709273147
50.00767863444370.0131099692558-0.05067861748120.0664255809980.05892324340130.112211958529-0.02376381134980.09770492249460.0441439098809-0.01909624253490.3908054614840.368513964464-0.218793341455-0.2088578470450.02668343397140.2788581392820.0637820012043-0.0114840122580.3081189527340.06529772841010.200274292309-24.137614375621.6802222805-26.9751328861
60.0418820232542-0.03004449935540.1064068045460.156728720160.2326221682940.0941566602798-0.096941781509-0.160379688797-0.1177266917820.08068145937580.08333641985440.04107278027210.343239401619-0.3459301052570.1880974631780.136925885667-0.03692039649820.0350541422610.278713950321-0.01791490994110.138906176791-25.234643180210.1745871438-8.37715600361
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain A and resid 236:329AA236 - 3291 - 94
22chain A and resid 330:386AA330 - 38695 - 151
33chain A and resid 387:495AA387 - 495152 - 260
44chain A and resid 496:575AA496 - 575261 - 332
55chain T or chain DT - DB - E1 - 4
66chain U or chain PU - PC - D1 - 7

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more