[English] 日本語
Yorodumi
- PDB-7o1f: PCNA from Chaetomium thermophilum in complex with PolD4 PIP peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7o1f
TitlePCNA from Chaetomium thermophilum in complex with PolD4 PIP peptide
Components
  • Peptide fragment from PolD4
  • Proliferating cell nuclear antigen
KeywordsREPLICATION / PCNA / DNA clamp / DNA replication / PIP / homotrimer / PolD4
Function / homology
Function and homology information


PCNA complex / DNA synthesis involved in DNA repair / DNA polymerase processivity factor activity / leading strand elongation / regulation of DNA replication / mismatch repair / translesion synthesis / DNA replication / DNA binding
Similarity search - Function
DNA polymerase delta, subunit 4 / DNA polymerase delta, subunit 4 / Proliferating cell nuclear antigen signature 2. / Proliferating cell nuclear antigen, PCNA, conserved site / Proliferating cell nuclear antigen signature 1. / Proliferating cell nuclear antigen, PCNA / Proliferating cell nuclear antigen, PCNA, N-terminal / Proliferating cell nuclear antigen, PCNA, C-terminal / Proliferating cell nuclear antigen, N-terminal domain / Proliferating cell nuclear antigen, C-terminal domain / :
Similarity search - Domain/homology
DNA polymerase delta subunit 4-like protein / Proliferating cell nuclear antigen
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.45 Å
AuthorsAlphey, M.A. / MacNeill, S. / Yang, D.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Other privateRIG 70668 United Kingdom
CitationJournal: Febs J. / Year: 2023
Title: Non-canonical binding of the Chaetomium thermophilum PolD4 N-terminal PIP motif to PCNA involves Q-pocket and compact 2-fork plug interactions but no 3 10 helix.
Authors: Yang, D. / Alphey, M.S. / MacNeill, S.A.
History
DepositionMar 29, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 5, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jan 11, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
J: Peptide fragment from PolD4
K: Peptide fragment from PolD4
M: Peptide fragment from PolD4
O: Peptide fragment from PolD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,26228
Polymers179,84810
Non-polymers41418
Water2,882160
1
A: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
J: Peptide fragment from PolD4
K: Peptide fragment from PolD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,10813
Polymers89,9245
Non-polymers1848
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7230 Å2
ΔGint-107 kcal/mol
Surface area33080 Å2
MethodPISA
2
D: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
M: Peptide fragment from PolD4
O: Peptide fragment from PolD4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,15415
Polymers89,9245
Non-polymers23010
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-127 kcal/mol
Surface area33270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.891, 84.711, 84.890
Angle α, β, γ (deg.)60.940, 89.600, 81.220
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16B
26C
17B
27D
18B
28E
19B
29F
110C
210D
111C
211E
112C
212F
113D
213E
114D
214F
115E
215F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAILEILEAA1 - 2553 - 257
21ALAALAILEILEBB1 - 2553 - 257
12ALAALAPROPROAA1 - 2533 - 255
22ALAALAPROPROCC1 - 2533 - 255
13ALAALAILEILEAA1 - 2553 - 257
23ALAALAILEILEDD1 - 2553 - 257
14ALAALAILEILEAA1 - 2553 - 257
24ALAALAILEILEEE1 - 2553 - 257
15ALAALAILEILEAA1 - 2553 - 257
25ALAALAILEILEFF1 - 2553 - 257
16ALAALAPROPROBB1 - 2533 - 255
26ALAALAPROPROCC1 - 2533 - 255
17ALAALAILEILEBB1 - 2553 - 257
27ALAALAILEILEDD1 - 2553 - 257
18ALAALAILEILEBB1 - 2553 - 257
28ALAALAILEILEEE1 - 2553 - 257
19ALAALAILEILEBB1 - 2553 - 257
29ALAALAILEILEFF1 - 2553 - 257
110ALAALAPROPROCC1 - 2533 - 255
210ALAALAPROPRODD1 - 2533 - 255
111ALAALAPROPROCC1 - 2533 - 255
211ALAALAPROPROEE1 - 2533 - 255
112ALAALAPROPROCC1 - 2533 - 255
212ALAALAPROPROFF1 - 2533 - 255
113ALAALAILEILEDD1 - 2553 - 257
213ALAALAILEILEEE1 - 2553 - 257
114METMETILEILEDD0 - 2552 - 257
214METMETILEILEFF0 - 2552 - 257
115ALAALAILEILEEE1 - 2553 - 257
215ALAALAILEILEFF1 - 2553 - 257

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

-
Components

#1: Protein
Proliferating cell nuclear antigen


Mass: 28756.596 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Details: The first 3 residues are the remaining linker after His-tag cleavage. Flexible loops and sidechains have been omitted or truncated
Source: (gene. exp.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719 / Gene: CTHT_0061010 / Plasmid: pEHISTEV-CtPCNA / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta 2 pLysS / References: UniProt: G0SF70
#2: Protein/peptide
Peptide fragment from PolD4


Mass: 1827.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Details: Flexible C-terminus unresolved in electron density
Source: (synth.) Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
References: UniProt: G0RZ52
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2 M Calcium acetate hydrate, 0.1 M Sodium cacodylate, pH 6.5, 36 % v/v PEG 300

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 2, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 2.45→30.39 Å / Num. obs: 59727 / % possible obs: 94.2 % / Redundancy: 3.9 % / CC1/2: 0.994 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.076 / Rrim(I) all: 0.151 / Net I/σ(I): 7.2 / Num. measured all: 230753 / Scaling rejects: 45
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.45-2.523.61.3681622545570.4060.8411.610.892.1
10.68-30.393.90.04827907110.9960.0280.05523.992.7

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
REFMAC5.8.0238refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O1E

7o1e


Resolution: 2.45→30.39 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.905 / SU B: 26.576 / SU ML: 0.272 / SU R Cruickshank DPI: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.59 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2619 2829 4.7 %RANDOM
Rwork0.2202 ---
obs0.2221 56897 94.16 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso max: 118.19 Å2 / Biso mean: 43.964 Å2 / Biso min: 23.42 Å2
Baniso -1Baniso -2Baniso -3
1-1.51 Å20.94 Å2-2.29 Å2
2--1.3 Å20.95 Å2
3----0.67 Å2
Refinement stepCycle: final / Resolution: 2.45→30.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11435 0 18 160 11613
Biso mean--46.95 43.14 -
Num. residues----1525
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01311566
X-RAY DIFFRACTIONr_bond_other_d0.0010.01710872
X-RAY DIFFRACTIONr_angle_refined_deg1.4611.63115661
X-RAY DIFFRACTIONr_angle_other_deg1.2261.57325206
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.77351501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.1624.399491
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.553152016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7461541
X-RAY DIFFRACTIONr_chiral_restr0.060.21642
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212786
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022129
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A71700.06
12B71700.06
21A67340.06
22C67340.06
31A72790.05
32D72790.05
41A70860.05
42E70860.05
51A73630.05
52F73630.05
61B67740.06
62C67740.06
71B71770.05
72D71770.05
81B70720.06
82E70720.06
91B71870.06
92F71870.06
101C67450.06
102D67450.06
111C67930.05
112E67930.05
121C67130.06
122F67130.06
131D71640.04
132E71640.04
141D72350.05
142F72350.05
151E70690.05
152F70690.05
LS refinement shellResolution: 2.45→2.513 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 231 -
Rwork0.346 4071 -
all-4302 -
obs--91.98 %
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)
10.63070.17320.05914.38620.85040.8134-0.02830.06030.0474-0.16190.05710.0011-0.04960.0096-0.02880.1267-0.04910.12370.1512-0.08060.2196-0.657-41.233-74.065
21.15880.13660.52432.233-2.05035.23060.0784-0.2135-0.07970.1491-0.094-0.09980.0365-0.06590.01560.1009-0.09190.11570.1053-0.09510.23943.996-26.545-33.634
31.32070.88240.45562.32271.26464.25420.25410.06-0.03130.4799-0.2131-0.2190.24620.1579-0.04110.3286-0.11160.0650.0893-0.02190.28970.681-68.665-41.524
41.2981-0.40560.33731.815-1.76254.8852-0.04140.06120.0896-0.0223-0.0524-0.0343-0.19610.04540.09390.087-0.05350.12820.0431-0.09660.2896-30.359-20.581-37.6
51.4038-0.0879-0.29674.73340.3121.1830.1198-0.0022-0.0617-0.1446-0.0740.1645-0.0545-0.083-0.04590.1183-0.05670.08270.0906-0.09260.2392-34.909-47.413-70.606
60.37520.01560.55732.28482.37983.496-0.0177-0.0986-0.02360.31650.0240.2450.411-0.1697-0.00630.3552-0.11880.13790.0908-0.00640.4085-31.985-63.153-30.775
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION2B1 - 255
3X-RAY DIFFRACTION3C1 - 253
4X-RAY DIFFRACTION4D0 - 255
5X-RAY DIFFRACTION5E1 - 255
6X-RAY DIFFRACTION6F0 - 255

+
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