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- PDB-2q9q: The crystal structure of full length human GINS complex -

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Basic information

Entry
Database: PDB / ID: 2q9q
TitleThe crystal structure of full length human GINS complex
Components
  • DNA replication complex GINS protein PSF1
  • DNA replication complex GINS protein PSF2
  • GINS complex subunit 3
  • GINS complex subunit 4
KeywordsREPLICATION / elongated spindle / helix bundle
Function / homology
Function and homology information


Unwinding of DNA / DNA strand elongation involved in mitotic DNA replication / GINS complex / CMG complex / double-strand break repair via break-induced replication / mitotic DNA replication initiation / inner cell mass cell proliferation / DNA unwinding involved in DNA replication / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1020 / Ribosomal Protein L9; domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2050 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Ribosomal Protein L9; domain 1 - #50 / Ribosomal Protein L9; domain 1 / DNA replication complex GINS protein Psf2 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1020 / Ribosomal Protein L9; domain 1 - #60 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #2050 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #1030 / Ribosomal Protein L9; domain 1 - #50 / Ribosomal Protein L9; domain 1 / DNA replication complex GINS protein Psf2 / GINS complex, subunit Psf1 / GINS complex, subunit Psf3 / GINS complex, subunit Psf3 superfamily / DNA replication complex GINS protein SLD5, C-terminal / GINS, helical bundle-like domain superfamily / GINS complex protein Sld5, alpha-helical domain / DNA replication complex GINS protein SLD5 C-terminus / GINS complex subunit Sld5 / GINS subunit, domain A / GINS complex protein / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
DNA replication complex GINS protein PSF1 / DNA replication complex GINS protein SLD5 / DNA replication complex GINS protein PSF3 / DNA replication complex GINS protein PSF2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.36 Å
AuthorsChang, Y.P. / Wang, G. / Chen, X.S.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2007
Title: Crystal structure of the GINS complex and functional insights into its role in DNA replication.
Authors: Chang, Y.P. / Wang, G. / Bermudez, V. / Hurwitz, J. / Chen, X.S.
History
DepositionJun 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA replication complex GINS protein PSF2
B: GINS complex subunit 4
C: DNA replication complex GINS protein PSF1
D: GINS complex subunit 3
E: DNA replication complex GINS protein PSF2
F: GINS complex subunit 4
G: DNA replication complex GINS protein PSF1
H: GINS complex subunit 3


Theoretical massNumber of molelcules
Total (without water)191,7098
Polymers191,7098
Non-polymers00
Water8,161453
1
A: DNA replication complex GINS protein PSF2
B: GINS complex subunit 4
C: DNA replication complex GINS protein PSF1
D: GINS complex subunit 3


Theoretical massNumber of molelcules
Total (without water)95,8544
Polymers95,8544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14460 Å2
ΔGint-108 kcal/mol
Surface area32150 Å2
MethodPISA, PQS
2
E: DNA replication complex GINS protein PSF2
F: GINS complex subunit 4
G: DNA replication complex GINS protein PSF1
H: GINS complex subunit 3


Theoretical massNumber of molelcules
Total (without water)95,8544
Polymers95,8544
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14610 Å2
ΔGint-110 kcal/mol
Surface area31900 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.269, 89.096, 103.800
Angle α, β, γ (deg.)105.02, 103.58, 95.07
Int Tables number1
Space group name H-MP1

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Components

#1: Protein DNA replication complex GINS protein PSF2


Mass: 21979.271 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS2, PSF2 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q9Y248
#2: Protein GINS complex subunit 4


Mass: 26081.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS4 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q9BRT9
#3: Protein DNA replication complex GINS protein PSF1


Mass: 23036.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS1, KIAA0186, PSF1 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q14691
#4: Protein GINS complex subunit 3 / Psf3 homolog


Mass: 24756.740 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GINS3 / Plasmid: pGEX6P-1 / Production host: Escherichia coli (E. coli) / Strain (production host): XA90 / References: UniProt: Q9BRX5
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 453 / 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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 60mM MES (pH5.5),2% (v/v) isopropanol, 34mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97932, 0.97945
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 21, 2006
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979321
20.979451
ReflectionResolution: 2.36→50 Å / Num. obs: 143641 / % possible obs: 98.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.12
Reflection shellResolution: 2.36→2.44 Å / Redundancy: 3.9 % / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.36→29.58 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 83176.35 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.248 12249 8.5 %RANDOM
Rwork0.21 ---
obs0.21 143641 90.6 %-
all-158544 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 58.2406 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 36.3 Å2
Baniso -1Baniso -2Baniso -3
1-2.53 Å24.28 Å20.27 Å2
2---3.73 Å2-4.46 Å2
3---1.2 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.36→29.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11430 0 0 453 11883
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d20.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it3.71.5
X-RAY DIFFRACTIONc_mcangle_it5.982
X-RAY DIFFRACTIONc_scbond_it5.422
X-RAY DIFFRACTIONc_scangle_it8.252.5
LS refinement shellResolution: 2.36→2.51 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.284 93 0.5 %
Rwork0.273 20340 -
obs--77.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top

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