[English] 日本語
Yorodumi
- PDB-6qcg: PCNA complex with Cdt1 N-terminal PIP-box peptide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6qcg
TitlePCNA complex with Cdt1 N-terminal PIP-box peptide
Components
  • DNA replication factor Cdt1
  • Proliferating cell nuclear antigen
KeywordsCELL CYCLE / dna replication / ubiquitination / clr4
Function / homology
Function and homology information


DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / Switching of origins to a post-replicative state / regulation of nuclear cell cycle DNA replication / negative regulation of DNA-templated DNA replication / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication ...DNA replication preinitiation complex assembly / response to sorbitol / positive regulation of DNA-templated DNA replication / Switching of origins to a post-replicative state / regulation of nuclear cell cycle DNA replication / negative regulation of DNA-templated DNA replication / positive regulation of deoxyribonuclease activity / dinucleotide insertion or deletion binding / PCNA-p21 complex / mitotic telomere maintenance via semi-conservative replication / purine-specific mismatch base pair DNA N-glycosylase activity / nuclear lamina / MutLalpha complex binding / positive regulation of DNA-directed DNA polymerase activity / Polymerase switching / Telomere C-strand (Lagging Strand) Synthesis / Processive synthesis on the lagging strand / DNA replication checkpoint signaling / PCNA complex / attachment of mitotic spindle microtubules to kinetochore / Removal of the Flap Intermediate / Processive synthesis on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta) / Polymerase switching on the C-strand of the telomere / Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha) / Transcription of E2F targets under negative control by DREAM complex / Removal of the Flap Intermediate from the C-strand / replisome / positive regulation of chromatin binding / regulation of DNA-templated DNA replication initiation / response to L-glutamate / histone acetyltransferase binding / DNA polymerase processivity factor activity / G1/S-Specific Transcription / leading strand elongation / response to dexamethasone / replication fork processing / nuclear replication fork / SUMOylation of DNA replication proteins / negative regulation of cell cycle / Activation of the pre-replicative complex / estrous cycle / PCNA-Dependent Long Patch Base Excision Repair / cyclin-dependent protein kinase holoenzyme complex / mismatch repair / translesion synthesis / response to cadmium ion / DNA polymerase binding / epithelial cell differentiation / positive regulation of DNA repair / Translesion synthesis by REV1 / Translesion synthesis by POLK / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / base-excision repair, gap-filling / TP53 Regulates Transcription of Genes Involved in G2 Cell Cycle Arrest / replication fork / positive regulation of DNA replication / male germ cell nucleus / Assembly of the pre-replicative complex / liver regeneration / nuclear estrogen receptor binding / Recognition of DNA damage by PCNA-containing replication complex / Termination of translesion DNA synthesis / Translesion Synthesis by POLH / HDR through Homologous Recombination (HRR) / Dual Incision in GG-NER / receptor tyrosine kinase binding / kinetochore / cellular response to hydrogen peroxide / Orc1 removal from chromatin / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / cellular response to UV / cellular response to xenobiotic stimulus / E3 ubiquitin ligases ubiquitinate target proteins / response to estradiol / heart development / mitotic cell cycle / chromosome, telomeric region / damaged DNA binding / nuclear body / cell division / centrosome / chromatin binding / protein-containing complex binding / chromatin / enzyme binding / negative regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 ...CDT1 Geminin-binding domain-like / DNA replication factor Cdt1 / DNA replication factor CDT1 like / DNA replication factor CDT1 like / DNA replication factor Cdt1, C-terminal / DNA replication factor Cdt1, C-terminal WH domain superfamily / DNA replication factor Cdt1 C-terminal domain / Box / Proliferating Cell Nuclear Antigen / Proliferating Cell Nuclear Antigen - #10 / 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 / : / Winged helix DNA-binding domain superfamily / Alpha Beta
Similarity search - Domain/homology
Proliferating cell nuclear antigen / DNA replication factor Cdt1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å
AuthorsPerrakis, A. / von Castelmur, E.
CitationJournal: Life Sci Alliance / Year: 2018
Title: Direct binding of Cdt2 to PCNA is important for targeting the CRL4Cdt2E3 ligase activity to Cdt1.
Authors: Hayashi, A. / Giakoumakis, N.N. / Heidebrecht, T. / Ishii, T. / Panagopoulos, A. / Caillat, C. / Takahara, M. / Hibbert, R.G. / Suenaga, N. / Stadnik-Spiewak, M. / Takahashi, T. / Shiomi, Y. ...Authors: Hayashi, A. / Giakoumakis, N.N. / Heidebrecht, T. / Ishii, T. / Panagopoulos, A. / Caillat, C. / Takahara, M. / Hibbert, R.G. / Suenaga, N. / Stadnik-Spiewak, M. / Takahashi, T. / Shiomi, Y. / Taraviras, S. / von Castelmur, E. / Lygerou, Z. / Perrakis, A. / Nishitani, H.
History
DepositionDec 28, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
E: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
I: DNA replication factor Cdt1
G: DNA replication factor Cdt1
H: DNA replication factor Cdt1
J: DNA replication factor Cdt1
K: DNA replication factor Cdt1
L: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)184,93812
Polymers184,93812
Non-polymers00
Water362
1
A: Proliferating cell nuclear antigen
C: Proliferating cell nuclear antigen
B: Proliferating cell nuclear antigen
I: DNA replication factor Cdt1
G: DNA replication factor Cdt1
H: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)92,4696
Polymers92,4696
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8180 Å2
ΔGint-37 kcal/mol
Surface area33970 Å2
MethodPISA
2
E: Proliferating cell nuclear antigen
D: Proliferating cell nuclear antigen
F: Proliferating cell nuclear antigen
J: DNA replication factor Cdt1
K: DNA replication factor Cdt1
L: DNA replication factor Cdt1


Theoretical massNumber of molelcules
Total (without water)92,4696
Polymers92,4696
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-36 kcal/mol
Surface area34430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.585, 143.173, 173.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12A
22B
13A
23E
14A
24D
15A
25F
16C
26B
17C
27E
18C
28D
19C
29F
110B
210E
111B
211D
112B
212F
113E
213D
114E
214F
115D
215F

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 255
2010C1 - 255
1020A1 - 255
2020B1 - 255
1030A1 - 255
2030E1 - 255
1040A1 - 255
2040D1 - 255
1050A1 - 255
2050F1 - 255
1060C1 - 255
2060B1 - 255
1070C1 - 255
2070E1 - 255
1080C1 - 255
2080D1 - 255
1090C1 - 255
2090F1 - 255
10100B1 - 255
20100E1 - 255
10110B1 - 255
20110D1 - 255
10120B1 - 254
20120F1 - 254
10130E1 - 255
20130D1 - 255
10140E1 - 254
20140F1 - 254
10150D1 - 255
20150F1 - 255

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 / PCNA / Cyclin


Mass: 28949.912 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PCNA / Production host: Escherichia coli (E. coli) / References: UniProt: P12004
#2: Protein/peptide
DNA replication factor Cdt1 / Double parked homolog / DUP


Mass: 1873.170 Da / Num. of mol.: 6 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9H211
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.2 %
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 15% (w/v) PEG 400, 100 mM calcium acetate, 100 mM MES/HCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.0003 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Apr 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0003 Å / Relative weight: 1
ReflectionResolution: 3.4→47.72 Å / Num. obs: 26813 / % possible obs: 99.3 % / Redundancy: 3.4 % / Net I/σ(I): 7.6
Reflection shellResolution: 3.4→3.63 Å / Mean I/σ(I) obs: 1.9 / CC1/2: 0.647 / % possible all: 99.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→46.21 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.884 / SU B: 78.738 / SU ML: 0.525 / Cross valid method: THROUGHOUT / ESU R Free: 0.606 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25308 1333 5 %RANDOM
Rwork0.20595 ---
obs0.20826 25428 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 77.834 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20 Å20 Å2
2---1.17 Å20 Å2
3---0.58 Å2
Refinement stepCycle: 1 / Resolution: 3.4→46.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12122 0 0 2 12124
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312283
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711625
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.63316580
X-RAY DIFFRACTIONr_angle_other_deg1.1951.57726993
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.00351563
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.5123.414580
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.516152248
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.1311564
X-RAY DIFFRACTIONr_chiral_restr0.0650.21656
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213604
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022380
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.1684.2146297
X-RAY DIFFRACTIONr_mcbond_other2.1684.2156296
X-RAY DIFFRACTIONr_mcangle_it3.7586.3237845
X-RAY DIFFRACTIONr_mcangle_other3.7586.3237846
X-RAY DIFFRACTIONr_scbond_it2.2584.4735986
X-RAY DIFFRACTIONr_scbond_other2.2584.4735987
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9076.6158736
X-RAY DIFFRACTIONr_long_range_B_refined6.63647.90712288
X-RAY DIFFRACTIONr_long_range_B_other6.63647.90512289
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

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

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A70810.08
12C70810.08
21A71140.08
22B71140.08
31A71630.08
32E71630.08
41A71130.06
42D71130.06
51A69990.09
52F69990.09
61C71130.08
62B71130.08
71C70860.08
72E70860.08
81C71260.07
82D71260.07
91C70260.09
92F70260.09
101B72630.08
102E72630.08
111B71150.06
112D71150.06
121B71670.1
122F71670.1
131E71390.07
132D71390.07
141E71160.1
142F71160.1
151D69920.09
152F69920.09
LS refinement shellResolution: 3.4→3.488 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 114 -
Rwork0.323 1842 -
obs--98.54 %
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)
12.3192-2.8159-0.47236.18480.69542.330.0330.4214-0.1242-0.6055-0.322-0.1471-0.13930.12210.2890.442-0.1260.00120.38150.02450.360977.2957.062172.068
21.099-0.728-0.09212.87932.14647.7042-0.09720.0836-0.1004-0.05730.0502-0.11910.45780.17940.0470.1180.0180.08320.07180.01660.535184.061-17.099208.083
31.2771-0.20050.25956.5194-4.13655.9417-0.23020.103-0.05990.09160.16650.2573-0.321-0.04880.06370.14040.0046-0.07750.0282-0.05850.357967.3722.886211.41
41.914-0.5213-0.68116.23922.69354.4279-0.2774-0.0697-0.02630.11180.24080.00130.16660.06710.03660.10090.01840.05180.01470.03860.483148.049-25.07213.467
52.1327-2.55410.82043.942-1.2112.9280.05630.275-0.0504-0.5515-0.320.1761-0.0277-0.04420.26370.4942-0.0425-0.10670.3333-0.14660.51348.238-16.232170.688
61.2853-0.4707-1.43912.0879-0.9716.8792-0.05080.1468-0.0588-0.289-0.05090.3484-0.1707-0.31740.10170.24170.0611-0.1440.0802-0.09560.625233.25313.289198.922
76.3573-2.06011.45612.6413-8.165832.23030.44610.011-0.6648-0.1859-0.18890.58050.20841.1691-0.25720.7815-0.0263-0.05110.37370.15821.087376.697-33.995204.057
81.598-3.5903-2.368213.89432.155.26090.08810.2563-0.0778-0.23860.05890.8691-0.1051-0.8023-0.1470.5670.0622-0.01930.4836-0.06290.901351.55820.626222.393
92.0448-3.3987-6.18736.052610.483619.48520.36440.27090.3078-0.28380.249-0.5631-0.1894-0.782-0.61341.25660.1977-0.03171.3133-0.16560.861262.02610.234161.284
102.4218-3.2430.5484.3574-0.73920.14480.0892-0.1045-0.1601-0.26490.10120.19940.09560.0426-0.19041.07590.1797-0.10051.4452-0.1171.191265.76-20.772164.883
1110.1583-14.5942-14.429821.084520.404822.8794-0.807-0.1046-0.15710.99310.00930.15380.73460.690.79770.8573-0.0223-0.00180.37140.01810.660342.52229.659193.99
120.7681-1.11412.522811.5574-10.001512.50840.47510.05680.14740.6083-1.3743-0.80760.49930.91840.89920.72680.06840.01270.4622-0.04890.751260.396-20.672227.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 255
2X-RAY DIFFRACTION2C1 - 255
3X-RAY DIFFRACTION3B1 - 255
4X-RAY DIFFRACTION4E1 - 255
5X-RAY DIFFRACTION5D1 - 255
6X-RAY DIFFRACTION6F-1 - 255
7X-RAY DIFFRACTION7I4 - 13
8X-RAY DIFFRACTION8G4 - 13
9X-RAY DIFFRACTION9H4 - 13
10X-RAY DIFFRACTION10J4 - 13
11X-RAY DIFFRACTION11K4 - 13
12X-RAY DIFFRACTION12L4 - 13

+
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://pdbjlvh1.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