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- PDB-2eho: Crystal structure of human GINS complex -

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Basic information

Entry
Database: PDB / ID: 2eho
TitleCrystal structure of human GINS complex
Components
  • (DNA replication complex GINS protein ...) x 2
  • (GINS complex subunit ...) x 2
KeywordsREPLICATION / protein-protein complex / 4-helical bundle / hydrophobic interaction
Function / homology
Function and homology information


Unwinding of DNA / GINS complex / DNA strand elongation involved in mitotic DNA replication / CMG complex / mitotic DNA replication initiation / double-strand break repair via break-induced replication / 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 helical bundle domain / 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 / SAD / Resolution: 3 Å
AuthorsChoi, J.M. / Lim, H.S. / Kim, J.J. / Song, O.K. / Cho, Y.
CitationJournal: Genes Dev. / Year: 2007
Title: Crystal structure of the human GINS complex
Authors: Choi, J.M. / Lim, H.S. / Kim, J.J. / Song, O.K. / Cho, Y.
History
DepositionMar 7, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 19, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Remark 999SEQUENCE THERE IS A DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. SWISSPROT SHOWS V -> I ...SEQUENCE THERE IS A DIFFERENCE BETWEEN THE SEQRES AND THE SEQUENCE DATABASE. SWISSPROT SHOWS V -> I (in Ref. 3) AT THIS POSITION.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GINS complex subunit 4
B: DNA replication complex GINS protein PSF1
C: DNA replication complex GINS protein PSF2
D: GINS complex subunit 3
E: GINS complex subunit 4
F: DNA replication complex GINS protein PSF1
G: DNA replication complex GINS protein PSF2
H: GINS complex subunit 3
I: GINS complex subunit 4
J: DNA replication complex GINS protein PSF1
K: DNA replication complex GINS protein PSF2
L: GINS complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,08629
Polymers268,45312
Non-polymers1,63317
Water2,432135
1
A: GINS complex subunit 4
B: DNA replication complex GINS protein PSF1
C: DNA replication complex GINS protein PSF2
D: GINS complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6766
Polymers89,4844
Non-polymers1922
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13560 Å2
ΔGint-136 kcal/mol
Surface area30880 Å2
MethodPISA
2
E: GINS complex subunit 4
F: DNA replication complex GINS protein PSF1
G: DNA replication complex GINS protein PSF2
H: GINS complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,25312
Polymers89,4844
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15950 Å2
ΔGint-216 kcal/mol
Surface area32290 Å2
MethodPISA
3
I: GINS complex subunit 4
J: DNA replication complex GINS protein PSF1
K: DNA replication complex GINS protein PSF2
L: GINS complex subunit 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,15711
Polymers89,4844
Non-polymers6727
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15830 Å2
ΔGint-197 kcal/mol
Surface area32050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)164.935, 176.995, 126.508
Angle α, β, γ (deg.)90.00, 105.91, 90.00
Int Tables number5
Space group name H-MC121
DetailsThe biological assembly is a tetramer constituted by each of 4 chains in the asymmetric unit, A-D,E-H, and I-L.

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Components

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GINS complex subunit ... , 2 types, 6 molecules AEIDHL

#1: Protein GINS complex subunit 4 / Sld5 homolog


Mass: 24354.615 Da / Num. of mol.: 3 / Fragment: Sld5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pACYC-duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BRT9
#4: Protein GINS complex subunit 3 / Psf3 homolog


Mass: 24843.982 Da / Num. of mol.: 3 / Fragment: Psf3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Psf3 / Plasmid: pCOLA-duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BRX5

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DNA replication complex GINS protein ... , 2 types, 6 molecules BFJCGK

#2: Protein DNA replication complex GINS protein PSF1 / Psf1


Mass: 18278.793 Da / Num. of mol.: 3 / Fragment: Psf1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Psf1 / Plasmid: pCDF-duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q14691
#3: Protein DNA replication complex GINS protein PSF2 / Psf2


Mass: 22006.967 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PSF2 / Plasmid: pET-duet / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9Y248

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Non-polymers , 2 types, 152 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.79 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1M Tris HCl, 1.8M ammonium sulfate, 0.2M lithium sulfate, 1.5% 1,2,3,-heptanetriol , pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1931
2931
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPAL/PLS 4A10.9795
SYNCHROTRONPAL/PLS 4A21
Detector
TypeIDDetectorDate
ADSC QUANTUM 2101CCDSep 20, 2006
ADSC QUANTUM 2102CCDSep 30, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97951
211
ReflectionResolution: 2.81→50 Å / Num. all: 83938 / Num. obs: 77549 / % possible obs: 98.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 31 Å2 / Rsym value: 0.0115 / Net I/σ(I): 18
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 3 / Num. unique all: 6734 / Rsym value: 0.302 / % possible all: 97.7

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: SAD / Resolution: 3→29.9 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 65022.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.274 3895 5 %RANDOM
Rwork0.221 ---
all0.25 ---
obs0.221 69327 91.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.4844 Å2 / ksol: 0.337085 e/Å3
Displacement parametersBiso mean: 58.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.89 Å20 Å2-2.03 Å2
2--8.66 Å20 Å2
3----6.77 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.51 Å0.45 Å
Refinement stepCycle: LAST / Resolution: 3→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16717 0 85 135 16937
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d21.2
X-RAY DIFFRACTIONc_improper_angle_d1.16
X-RAY DIFFRACTIONc_mcbond_it1.431.5
X-RAY DIFFRACTIONc_mcangle_it2.512
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.333 520 5.3 %
Rwork0.3 9313 -
obs-9313 69.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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