[English] 日本語
Yorodumi
- PDB-8rok: Human cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conforma... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8rok
TitleHuman cohesin SMC3-HD(EQ)/RAD21-N complex - ATP-Mg-bound conformation - Form 1
Components
  • Double-strand-break repair protein rad21 homolog
  • Structural maintenance of chromosomes protein 3
KeywordsNUCLEAR PROTEIN / 3D genome organization / Chromatin / Cohesin / ATPase activity / ATPase cycle
Function / homology
Function and homology information


negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process ...negative regulation of mitotic metaphase/anaphase transition / Cohesin Loading onto Chromatin / meiotic cohesin complex / Establishment of Sister Chromatid Cohesion / establishment of meiotic sister chromatid cohesion / cohesin complex / positive regulation of sister chromatid cohesion / mitotic cohesin complex / negative regulation of G2/M transition of mitotic cell cycle / negative regulation of glial cell apoptotic process / lateral element / mediator complex binding / replication-born double-strand break repair via sister chromatid exchange / establishment of mitotic sister chromatid cohesion / chromatin looping / reciprocal meiotic recombination / microtubule motor activity / sister chromatid cohesion / negative regulation of interleukin-1 beta production / mitotic sister chromatid cohesion / lncRNA binding / stem cell population maintenance / dynein complex binding / mitotic spindle pole / beta-tubulin binding / regulation of DNA replication / positive regulation of interleukin-10 production / chromosome, centromeric region / negative regulation of tumor necrosis factor production / mitotic spindle assembly / SUMOylation of DNA damage response and repair proteins / protein localization to chromatin / Resolution of Sister Chromatid Cohesion / Meiotic synapsis / condensed nuclear chromosome / meiotic cell cycle / chromosome segregation / spindle pole / nuclear matrix / Separation of Sister Chromatids / double-strand break repair / mitotic cell cycle / chromosome / midbody / double-stranded DNA binding / DNA-binding transcription factor binding / DNA recombination / Estrogen-dependent gene expression / negative regulation of neuron apoptotic process / response to hypoxia / protein heterodimerization activity / cell division / DNA repair / apoptotic process / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / ATP hydrolysis activity / DNA binding / nucleoplasm / ATP binding / nucleus / membrane / cytosol
Similarity search - Function
Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge ...Structural maintenance of chromosomes 3, ABC domain, eukaryotic / : / Rad21/Rec8-like protein, C-terminal, eukaryotic / Rad21/Rec8-like protein, N-terminal / Rad21/Rec8-like protein / Conserved region of Rad21 / Rec8 like protein / N terminus of Rad21 / Rec8 like protein / ScpA-like, C-terminal / Structural maintenance of chromosomes protein / SMCs flexible hinge / SMCs flexible hinge superfamily / SMC proteins Flexible Hinge Domain / SMC proteins Flexible Hinge Domain / RecF/RecN/SMC, N-terminal / RecF/RecN/SMC N terminal domain / Winged helix DNA-binding domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / Double-strand-break repair protein rad21 homolog / Structural maintenance of chromosomes protein 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsVitoria Gomes, M. / Romier, C.
Funding support France, 7items
OrganizationGrant numberCountry
Fondation ARCARCPJA20181208268 France
Fondation ARCARCPJA2021060003715 France
Fondation ARCDOC20180507150 France
Agence Nationale de la Recherche (ANR)ANR-10-LABX-030-INRT France
Agence Nationale de la Recherche (ANR)ANR-10-IDEX-0002 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0023 France
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-01 France
CitationJournal: Cell Rep / Year: 2024
Title: The cohesin ATPase cycle is mediated by specific conformational dynamics and interface plasticity of SMC1A and SMC3 ATPase domains.
Authors: Marina Vitoria Gomes / Pauline Landwerlin / Marie-Laure Diebold-Durand / Tajith B Shaik / Alexandre Durand / Edouard Troesch / Chantal Weber / Karl Brillet / Marianne Victoria Lemée / ...Authors: Marina Vitoria Gomes / Pauline Landwerlin / Marie-Laure Diebold-Durand / Tajith B Shaik / Alexandre Durand / Edouard Troesch / Chantal Weber / Karl Brillet / Marianne Victoria Lemée / Christophe Decroos / Ludivine Dulac / Pierre Antony / Erwan Watrin / Eric Ennifar / Christelle Golzio / Christophe Romier /
Abstract: Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we ...Cohesin is key to eukaryotic genome organization and acts throughout the cell cycle in an ATP-dependent manner. The mechanisms underlying cohesin ATPase activity are poorly understood. Here, we characterize distinct steps of the human cohesin ATPase cycle and show that the SMC1A and SMC3 ATPase domains undergo specific but concerted structural rearrangements along this cycle. Specifically, whereas the proximal coiled coil of the SMC1A ATPase domain remains conformationally stable, that of the SMC3 displays an intrinsic flexibility. The ATP-dependent formation of the heterodimeric SMC1A/SMC3 ATPase module (engaged state) favors this flexibility, which is counteracted by NIPBL and DNA binding (clamped state). Opening of the SMC3/RAD21 interface (open-engaged state) stiffens the SMC3 proximal coiled coil, thus constricting together with that of SMC1A the ATPase module DNA-binding chamber. The plasticity of the ATP-dependent interface between the SMC1A and SMC3 ATPase domains enables these structural rearrangements while keeping the ATP gate shut. VIDEO ABSTRACT.
History
DepositionJan 11, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 18, 2024Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 25, 2024Group: Structure summary / Category: struct / Item: _struct.title
Revision 1.3Mar 26, 2025Group: Structure summary / Category: pdbx_entry_details / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Structural maintenance of chromosomes protein 3
B: Double-strand-break repair protein rad21 homolog
C: Structural maintenance of chromosomes protein 3
D: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,1148
Polymers130,0194
Non-polymers1,0954
Water1,62190
1
A: Structural maintenance of chromosomes protein 3
B: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5574
Polymers65,0092
Non-polymers5482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-48 kcal/mol
Surface area21880 Å2
MethodPISA
2
C: Structural maintenance of chromosomes protein 3
D: Double-strand-break repair protein rad21 homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5574
Polymers65,0092
Non-polymers5482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5790 Å2
ΔGint-49 kcal/mol
Surface area22930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.244, 154.459, 136.541
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Structural maintenance of chromosomes protein 3 / SMC protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / ...SMC protein 3 / SMC-3 / Basement membrane-associated chondroitin proteoglycan / Bamacan / Chondroitin sulfate proteoglycan 6 / Chromosome-associated polypeptide / hCAP


Mass: 52391.367 Da / Num. of mol.: 2 / Mutation: E1144Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SMC3, BAM, BMH, CSPG6, SMC3L1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UQE7
#2: Protein Double-strand-break repair protein rad21 homolog / hHR21 / Nuclear matrix protein 1 / NXP-1 / SCC1 homolog


Mass: 12617.939 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RAD21, HR21, KIAA0078, NXP1, SCC1 / Production host: Escherichia coli (E. coli) / References: UniProt: O60216
#3: Chemical ChemComp-AGS / PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-GAMMA-S / ADENOSINE 5'-(3-THIOTRIPHOSPHATE) / ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE) / ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE


Mass: 523.247 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3S / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP-gamma-S, energy-carrying molecule analogue*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 90 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.42 Å3/Da / Density % sol: 49.15 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.3 M NaCl; 0.05 M L-Arginine; 0.1 M Tris pH7.5; 22.5 % v/v PEG Smear Broad; 0.05 M L-Glutamic acid monosodium salt hydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.000002 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.000002 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. obs: 58135 / % possible obs: 98 % / Redundancy: 13.6 % / Biso Wilson estimate: 48.58 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.098 / Net I/σ(I): 20.32
Reflection shellResolution: 2.25→2.39 Å / Redundancy: 13.1 % / Rmerge(I) obs: 2.233 / Mean I/σ(I) obs: 1.34 / Num. unique obs: 8944 / CC1/2: 0.816 / % possible all: 94.2

-
Processing

Software
NameVersionClassification
PHENIX1.17_3644refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.25→47.21 Å / SU ML: 0.3738 / Cross valid method: FREE R-VALUE / σ(F): 0.38 / Phase error: 33.5302
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2526 5433 4.84 %
Rwork0.202 106724 -
obs0.2045 58103 98.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 74.7 Å2
Refinement stepCycle: LAST / Resolution: 2.25→47.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7587 0 0 90 7677
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00767724
X-RAY DIFFRACTIONf_angle_d0.927410373
X-RAY DIFFRACTIONf_chiral_restr0.05021149
X-RAY DIFFRACTIONf_plane_restr0.00521307
X-RAY DIFFRACTIONf_dihedral_angle_d20.7392950
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.280.57841270.47793017X-RAY DIFFRACTION81.54
2.28-2.30.42562000.38413464X-RAY DIFFRACTION97.58
2.3-2.330.4011630.35743566X-RAY DIFFRACTION98.26
2.33-2.360.41071520.33823604X-RAY DIFFRACTION97.89
2.36-2.390.35222350.3223515X-RAY DIFFRACTION97.96
2.39-2.430.37181960.31413554X-RAY DIFFRACTION97.96
2.43-2.460.37711730.2953524X-RAY DIFFRACTION98.3
2.46-2.50.37771650.28243626X-RAY DIFFRACTION98.26
2.5-2.540.35361700.27643558X-RAY DIFFRACTION98.13
2.54-2.580.36471840.28153617X-RAY DIFFRACTION98.47
2.58-2.620.32281460.26893548X-RAY DIFFRACTION98.27
2.62-2.670.31971610.27283543X-RAY DIFFRACTION98.3
2.67-2.720.32791930.25763580X-RAY DIFFRACTION98.46
2.72-2.780.32941980.24273570X-RAY DIFFRACTION98.33
2.78-2.840.31731830.25643548X-RAY DIFFRACTION98.52
2.84-2.90.33631810.25513576X-RAY DIFFRACTION98.35
2.9-2.980.29171650.23753562X-RAY DIFFRACTION98.65
2.98-3.060.30262050.23223594X-RAY DIFFRACTION99.11
3.06-3.150.27971890.22843572X-RAY DIFFRACTION98.64
3.15-3.250.27662010.2123598X-RAY DIFFRACTION99.29
3.25-3.360.22681770.20823598X-RAY DIFFRACTION98.93
3.36-3.50.25992090.20733553X-RAY DIFFRACTION99.13
3.5-3.660.26171950.20343594X-RAY DIFFRACTION99.11
3.66-3.850.27831980.18973549X-RAY DIFFRACTION98.87
3.85-4.090.19771360.17153647X-RAY DIFFRACTION98.88
4.09-4.410.19912020.15433626X-RAY DIFFRACTION99.58
4.41-4.850.20751810.14283585X-RAY DIFFRACTION99.52
4.85-5.550.20391830.15913600X-RAY DIFFRACTION99.66
5.55-6.990.23761770.18043664X-RAY DIFFRACTION99.74
6.99-47.210.17531880.14863572X-RAY DIFFRACTION99.13
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)
10.6199256435840.1744379695930.1448716653140.9912519136690.4602198599980.007189579822580.109394952128-0.0226580542499-0.04588674738020.0236425199296-0.0892532580574-0.00139702081411-0.145103309650.066282977969-0.0034811372980.3509118077560.02365054716540.05505201006570.33844400879-0.008834981090680.368372044368-35.978243755416.134056910526.7021167635
20.0663496357116-0.0267121953611-0.04146580055680.156546910351-0.06956144646930.06042658501370.1715621171650.261564647682-0.0805613696362-0.573411804181-0.214049780584-0.6196617163940.2473458650240.0338832617270.0004570286887720.6207161150740.04566073870790.1521839180840.529172371877-0.08135506023350.814964822237-47.9793561279-7.0681562929418.878433342
30.516249749412-0.64558314896-0.4112947676091.028678686930.7449236128340.7426102750290.08736510424220.07985118462810.00844991821311-0.144262214495-0.0983763118078-0.0908749649294-0.00434630899765-0.143781797531.4391144233E-50.425667839182-0.0520252077068-0.01776401589540.3951842252980.009607513348260.353287069597-37.574922122354.874576960147.8579910352
40.1724792047660.08460452835840.1277507436480.31323819534-0.0747867515160.1580629539610.297213674104-0.009675381108470.0348358785376-0.0608951852373-0.15398764508-0.318331898121-0.352057259693-0.2875085935630.0001084032600190.508686980810.0325979524642-0.06141080263590.537689160883-0.007948040923820.522462103723-49.677846478476.619664815155.0010242665
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

+
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