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- PDB-6igx: Crystal structure of human CAP-G in complex with CAP-H -

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Basic information

Entry
Database: PDB / ID: 6igx
TitleCrystal structure of human CAP-G in complex with CAP-H
Components
  • Condensin complex subunit 2
  • Condensin complex subunit 3
KeywordsCELL CYCLE / condensin I subunits / chromosome condensation / protein-protein interaction / heat repeats
Function / homology
Function and homology information


condensin complex / condensed chromosome, centromeric region / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / condensed chromosome / cell division / chromatin binding / nucleoplasm / membrane / nucleus ...condensin complex / condensed chromosome, centromeric region / mitotic chromosome condensation / Condensation of Prometaphase Chromosomes / condensed chromosome / cell division / chromatin binding / nucleoplasm / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Nuclear condensin complex subunit 3, C-terminal domain / Condensin complex subunit 3 / Nuclear condensing complex subunits, C-term domain / Condensin complex subunit 2/barren / Condensin complex subunit 2 / Armadillo-like helical / Armadillo-type fold
Similarity search - Domain/homology
Condensin complex subunit 2 / Condensin complex subunit 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.995 Å
AuthorsHara, K. / Migita, T. / Shimizu, K. / Hashimoto, H.
CitationJournal: Embo Rep. / Year: 2019
Title: Structural basis of HEAT-kleisin interactions in the human condensin I subcomplex.
Authors: Hara, K. / Kinoshita, K. / Migita, T. / Murakami, K. / Shimizu, K. / Takeuchi, K. / Hirano, T. / Hashimoto, H.
History
DepositionSep 26, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Data collection / 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
Revision 1.2May 22, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume / _citation_author.identifier_ORCID
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Condensin complex subunit 3
A: Condensin complex subunit 2
D: Condensin complex subunit 3
C: Condensin complex subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)202,6505
Polymers202,4124
Non-polymers2381
Water1086
1
B: Condensin complex subunit 3
A: Condensin complex subunit 2


Theoretical massNumber of molelcules
Total (without water)101,2062
Polymers101,2062
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-26 kcal/mol
Surface area37460 Å2
MethodPISA
2
D: Condensin complex subunit 3
C: Condensin complex subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,4443
Polymers101,2062
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-20 kcal/mol
Surface area37570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)122.433, 61.998, 130.885
Angle α, β, γ (deg.)90.00, 93.47, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Condensin complex subunit 3 / / Chromosome-associated protein G / Condensin subunit CAP-G / hCAP-G / Melanoma antigen NY-MEL-3 / ...Chromosome-associated protein G / Condensin subunit CAP-G / hCAP-G / Melanoma antigen NY-MEL-3 / Non-SMC condensin I complex subunit G / XCAP-G homolog


Mass: 94461.242 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Internal amino acid sequence (residues 479-553) truncated.
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAPG, CAPG, NYMEL3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BPX3
#2: Protein Condensin complex subunit 2 / / Barren homolog protein 1 / Chromosome-associated protein H / hCAP-H / Non-SMC condensin I complex ...Barren homolog protein 1 / Chromosome-associated protein H / hCAP-H / Non-SMC condensin I complex subunit H / XCAP-H homolog


Mass: 6744.526 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCAPH, BRRN, BRRN1, CAPH, KIAA0074 / Production host: Escherichia coli (E. coli) / References: UniProt: Q15003
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, HEPES-NaOH pH 7.5, Ethylen glycol, Magnesium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Dec 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.995→20 Å / Num. obs: 39494 / % possible obs: 98.6 % / Redundancy: 3.35 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rrim(I) all: 0.082 / Net I/σ(I): 13.8
Reflection shellResolution: 2.995→3.16 Å / Redundancy: 3.45 % / Rmerge(I) obs: 0.552 / Mean I/σ(I) obs: 2.07 / Num. unique obs: 6128 / CC1/2: 0.721 / Rrim(I) all: 0.653 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 2.995→19.81 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4
RfactorNum. reflection% reflection
Rfree0.2717 1981 5.02 %
Rwork0.212 --
obs0.215 39492 99.01 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.995→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12341 0 15 6 12362
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00212530
X-RAY DIFFRACTIONf_angle_d0.68416948
X-RAY DIFFRACTIONf_dihedral_angle_d14.3564720
X-RAY DIFFRACTIONf_chiral_restr0.0262076
X-RAY DIFFRACTIONf_plane_restr0.0032111
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9951-3.06980.37911470.3182549X-RAY DIFFRACTION96
3.0698-3.15250.35651460.30682662X-RAY DIFFRACTION100
3.1525-3.24480.40671310.29162701X-RAY DIFFRACTION100
3.2448-3.34910.36711450.29362674X-RAY DIFFRACTION100
3.3491-3.46820.31751790.26572635X-RAY DIFFRACTION100
3.4682-3.60620.32211560.25822689X-RAY DIFFRACTION100
3.6062-3.76930.33861360.24032635X-RAY DIFFRACTION100
3.7693-3.96650.26351420.22342702X-RAY DIFFRACTION99
3.9665-4.21280.2731390.20192694X-RAY DIFFRACTION99
4.2128-4.53450.24611420.19762686X-RAY DIFFRACTION99
4.5345-4.98420.23381460.18712666X-RAY DIFFRACTION99
4.9842-5.69040.25081040.20052747X-RAY DIFFRACTION99
5.6904-7.11370.27551450.22322710X-RAY DIFFRACTION99
7.1137-19.81040.17691230.1442761X-RAY DIFFRACTION97

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