[English] 日本語
Yorodumi
- PDB-7jl8: Human PrimPol extending from the correct primer base C opposite t... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7jl8
TitleHuman PrimPol extending from the correct primer base C opposite the 8-oxoguanine lesion
Components
  • DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
  • DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
  • DNA-directed primase/polymerase protein
KeywordsTRANSFERASE/DNA / Translesion / DNA synthesis / DNA Replication / DNA damage / TRANSFERASE / TRANSFERASE-DNA complex
Function / homology
Function and homology information


DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA replication, synthesis of primer / mitochondrial DNA repair / replication fork processing / error-prone translesion synthesis / translesion synthesis / response to UV / DNA-directed RNA polymerase complex ...DNA primase AEP / R-loop processing / mitochondrial DNA replication / DNA replication, synthesis of primer / mitochondrial DNA repair / replication fork processing / error-prone translesion synthesis / translesion synthesis / response to UV / DNA-directed RNA polymerase complex / replication fork / DNA-directed RNA polymerase activity / manganese ion binding / DNA-directed DNA polymerase / DNA-directed DNA polymerase activity / mitochondrial matrix / chromatin binding / mitochondrion / zinc ion binding / nucleus
Similarity search - Function
DNA-directed primase/polymerase protein / Herpesviridae UL52/UL70 DNA primase / DNA primase, small subunit / DNA primase small subunit
Similarity search - Domain/homology
2'-DEOXYADENOSINE 5'-TRIPHOSPHATE / DI(HYDROXYETHYL)ETHER / DNA / DNA (> 10) / DNA-directed primase/polymerase protein
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRechkoblit, O. / Aggarwal, A.K.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM131780 United States
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis of DNA synthesis opposite 8-oxoguanine by human PrimPol primase-polymerase.
Authors: Rechkoblit, O. / Johnson, R.E. / Gupta, Y.K. / Prakash, L. / Prakash, S. / Aggarwal, A.K.
History
DepositionJul 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Jul 14, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
H: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,33420
Polymers100,3916
Non-polymers1,94314
Water2,900161
1
A: DNA-directed primase/polymerase protein
C: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
D: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,18510
Polymers50,1953
Non-polymers9907
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: DNA-directed primase/polymerase protein
G: DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')
H: DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,14910
Polymers50,1953
Non-polymers9547
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.689, 65.330, 72.001
Angle α, β, γ (deg.)68.470, 85.670, 86.920
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein DNA-directed primase/polymerase protein / hPrimpol1 / Coiled-coil domain-containing protein 111


Mass: 41038.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRIMPOL, CCDC111 / Production host: Saccharomyces cerevisiae (brewer's yeast)
References: UniProt: Q96LW4, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases

-
DNA chain , 2 types, 4 molecules CGDH

#2: DNA chain DNA (5'-D(P*AP*TP*(8OG)P*CP*CP*TP*AP*CP*CP*AP*CP*A)-3')


Mass: 5053.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(P*GP*TP*GP*GP*TP*AP*GP*GP*C)-3')


Mass: 4103.655 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

-
Non-polymers , 6 types, 175 molecules

#4: Chemical ChemComp-DTP / 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#8: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 161 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 225-250 mM CaCl2, 16-19% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.03324 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 20, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03324 Å / Relative weight: 1
ReflectionResolution: 2.099→28.162 Å / Num. obs: 48622 / % possible obs: 97.1 % / Redundancy: 3.4 % / CC1/2: 0.998 / Net I/σ(I): 11.6
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 3825 / CC1/2: 0.78 / % possible all: 93.6

-
Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5L2X

5l2x


Resolution: 2.1→28.16 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 23.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2133 2308 4.75 %
Rwork0.1871 46258 -
obs0.1883 48566 97.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 220.87 Å2 / Biso mean: 65.1446 Å2 / Biso min: 26.2 Å2
Refinement stepCycle: final / Resolution: 2.1→28.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4059 807 217 161 5244
Biso mean--65.11 48.93 -
Num. residues----560
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.32161430.29182749289294
2.15-2.20.30271460.25812906305297
2.2-2.250.26431710.2362865303697
2.25-2.310.26711410.22752878301997
2.31-2.380.27091490.22122865301497
2.38-2.460.24961470.21142865301297
2.46-2.540.28021560.20572908306497
2.54-2.650.24491470.19962895304297
2.65-2.770.25051390.19382916305597
2.77-2.910.24021330.18992860299397
2.91-3.090.20321370.19412934307198
3.09-3.330.20331410.18372914305598
3.33-3.670.20331400.16662957309798
3.67-4.20.16581320.16492922305498
4.2-5.280.16131290.1562925305498
5.28-28.160.21991570.19882899305698
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)
13.00830.26510.03132.8605-0.37970.3781-0.43710.3574-0.858-0.62950.05321.03410.5642-0.711-0.54150.0384-0.1274-0.63440.3660.19180.830740.8304-60.1254-3.0686
23.03021.69271.06063.3262-0.8842.3289-0.0497-0.09360.6405-0.23020.21680.8322-0.188-0.0158-0.10540.28860.0277-0.06570.34010.02960.596248.2849-52.01833.2347
32.8350.0119-0.93463.03250.0051.53670.1131-0.41230.13510.4663-0.04010.036-0.23270.1367-0.09060.4117-0.02690.02640.3551-0.05890.30559.4003-62.803521.9404
42.5995-0.3362-0.78233.65580.50833.44260.20960.0914-0.11390.1782-0.00110.03230.01270.1587-0.1930.3928-0.01130.01780.3774-0.06670.414758.9373-71.598112.8234
53.00844.33241.29097.28290.06794.33970.3313-0.79280.36371.7172-0.47590.91710.3134-0.71690.08240.8634-0.15520.14040.5702-0.0650.374551.9867-70.593830.5708
62.3159-0.0502-0.20633.5674-0.66151.06330.0726-0.14780.2670.2984-0.08880.3935-0.0819-0.05370.00770.37670.00640.04350.4046-0.08440.381958.3582-53.341213.472
71.6021-1.98740.0342.77080.72671.66-0.03490.2645-0.1124-0.28240.1584-0.4120.31210.1168-0.08150.484-0.0020.04340.4749-0.06790.489862.903-69.17325.6305
82.57730.8145-1.23154.60552.02471.98880.9097-0.9967-0.32460.5555-0.58420.42211.3288-0.3279-0.56410.7149-0.3714-0.26930.8550.19141.046534.7253-72.288917.4444
92.7171.0463-0.76393.5237-0.85370.35050.34690.0885-0.4106-1.75350.66451.83071.7954-1.0092-0.67181.7145-0.5511-0.04820.950.18831.423433.926-74.631219.4316
104.2602-0.97020.61723.98460.01543.37590.26010.3365-0.2597-0.17750.00840.67790.1714-0.6852-0.16830.2649-0.0083-0.050.5299-0.01270.485649.9217-93.5894-12.7374
113.293-0.93880.98433.67750.32821.3437-0.07850.2086-0.47540.0285-0.00110.19060.3664-0.2733-0.00710.25760.0189-0.05120.3402-0.05840.325559.91-99.1122-11.924
123.4486-0.934-1.80142.04790.09922.8579-0.1134-0.0918-0.25820.11180.0483-0.1035-0.02270.24780.05190.2580.0115-0.02840.359-0.02650.321379.7993-87.9533-5.6929
134.4012-0.6864-0.85233.84441.20192.76250.0678-0.33480.19230.19620.01460.1936-0.1352-0.1864-0.08010.3130.0282-0.04170.3302-0.03190.327770.8619-79.2544-2.9889
142.61840.7933-0.86561.91710.02581.7166-0.0080.0704-0.0642-0.1544-0.0158-0.18360.03890.17610.05750.26970.0557-0.02170.4084-0.02850.340676.3245-91.4289-8.78
151.78980.57370.33732.49761.69462.00520.0684-0.17420.29840.3275-0.05390.2802-0.2592-0.0996-0.10180.43810.03210.06640.4294-0.05810.420965.1973-81.22991.8863
162.5997-1.4724-0.58941.6377-1.16443.3419-0.2830.57290.7457-1.3575-0.1789-0.5584-0.95870.5980.33770.912-0.1863-0.03140.79110.25070.59669.0525-78.2781-28.0604
173.0442-1.67010.27829.1677-1.10653.2178-0.02040.93470.0739-2.51620.30750.6846-0.922-0.1532-0.13681.3471-0.09220.07030.84680.30830.900668.6532-76.0963-30.8217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 47 )A1 - 47
2X-RAY DIFFRACTION2chain 'A' and (resid 48 through 102 )A48 - 102
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 172 )A103 - 172
4X-RAY DIFFRACTION4chain 'A' and (resid 173 through 192 )A173 - 192
5X-RAY DIFFRACTION5chain 'A' and (resid 193 through 280 )A193 - 280
6X-RAY DIFFRACTION6chain 'A' and (resid 281 through 330 )A281 - 330
7X-RAY DIFFRACTION7chain 'A' and (resid 331 through 348 )A331 - 348
8X-RAY DIFFRACTION8chain 'C' and (resid 2 through 13 )C2 - 13
9X-RAY DIFFRACTION9chain 'D' and (resid 6 through 14 )D6 - 14
10X-RAY DIFFRACTION10chain 'B' and (resid 38 through 58 )B38 - 58
11X-RAY DIFFRACTION11chain 'B' and (resid 59 through 102 )B59 - 102
12X-RAY DIFFRACTION12chain 'B' and (resid 103 through 172 )B103 - 172
13X-RAY DIFFRACTION13chain 'B' and (resid 173 through 192 )B173 - 192
14X-RAY DIFFRACTION14chain 'B' and (resid 193 through 330 )B193 - 330
15X-RAY DIFFRACTION15chain 'B' and (resid 331 through 348 )B331 - 348
16X-RAY DIFFRACTION16chain 'G' and (resid 3 through 12 )G3 - 12
17X-RAY DIFFRACTION17chain 'H' and (resid 6 through 14 )H6 - 14

+
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