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- PDB-3qor: Crystal structure of human nuclear migration protein NudC -

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Basic information

Entry
Database: PDB / ID: 3qor
TitleCrystal structure of human nuclear migration protein NudC
Components(Nuclear migration protein ...) x 4
KeywordsPROTEIN BINDING / CELL CYCLE / beta-sandwich / nuclear migration protein / chaperone
Function / homology
Function and homology information


RND2 GTPase cycle / nuclear migration / mitotic metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / RHO GTPases Activate Formins / response to peptide hormone ...RND2 GTPase cycle / nuclear migration / mitotic metaphase chromosome alignment / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / mitotic spindle organization / RHO GTPases Activate Formins / response to peptide hormone / spindle / mitotic spindle / Separation of Sister Chromatids / unfolded protein binding / protein folding / midbody / microtubule / cadherin binding / cell division / nucleoplasm / cytoplasm / cytosol
Similarity search - Function
Nuclear migration protein nudC / Nuclear distribution C domain / NudC N-terminal domain / N-terminal conserved domain of Nudc. / NudC family / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone ...Nuclear migration protein nudC / Nuclear distribution C domain / NudC N-terminal domain / N-terminal conserved domain of Nudc. / NudC family / CS domain / CS domain / CS domain profile. / Immunoglobulin-like - #790 / HSP20-like chaperone / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Nuclear migration protein nudC
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.753 Å
AuthorsDerewenda, U. / Derewenda, Z. / Zheng, M.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Structural Features and Chaperone Activity of the NudC Protein Family.
Authors: Zheng, M. / Cierpicki, T. / Burdette, A.J. / Utepbergenov, D. / Janczyk, P.L. / Derewenda, U. / Stukenberg, P.T. / Caldwell, K.A. / Derewenda, Z.S.
History
DepositionFeb 10, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 26, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear migration protein nudC
B: Nuclear migration protein nudC
C: Nuclear migration protein nudC
D: Nuclear migration protein nudC
E: Nuclear migration protein nudC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5166
Polymers68,4575
Non-polymers591
Water15,799877
1
A: Nuclear migration protein nudC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7382
Polymers13,6791
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear migration protein nudC


Theoretical massNumber of molelcules
Total (without water)13,6951
Polymers13,6951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Nuclear migration protein nudC


Theoretical massNumber of molelcules
Total (without water)13,6631
Polymers13,6631
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Nuclear migration protein nudC


Theoretical massNumber of molelcules
Total (without water)13,7111
Polymers13,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Nuclear migration protein nudC


Theoretical massNumber of molelcules
Total (without water)13,7111
Polymers13,7111
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)66.734, 51.820, 92.854
Angle α, β, γ (deg.)90.00, 90.58, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Nuclear migration protein ... , 4 types, 5 molecules ABCDE

#1: Protein Nuclear migration protein nudC / Nuclear distribution protein C homolog


Mass: 13678.567 Da / Num. of mol.: 1 / Fragment: residues 158-274 / Mutation: E236A, K129A
Source method: isolated from a genetically manipulated source
Details: Cys188 is modified to S-OXY CYSTEINE / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y266
#2: Protein Nuclear migration protein nudC / Nuclear distribution protein C homolog


Mass: 13694.566 Da / Num. of mol.: 1 / Fragment: residues 158-274 / Mutation: E236A, K129A
Source method: isolated from a genetically manipulated source
Details: Cys188 is modified to 3-SULFINOALANINE / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y266
#3: Protein Nuclear migration protein nudC / Nuclear distribution protein C homolog


Mass: 13662.567 Da / Num. of mol.: 1 / Fragment: residues 158-274 / Mutation: E236A, K129A
Source method: isolated from a genetically manipulated source
Details: Cys188 is unmodified / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y266
#4: Protein Nuclear migration protein nudC / Nuclear distribution protein C homolog


Mass: 13710.565 Da / Num. of mol.: 2 / Fragment: residues 158-274 / Mutation: E236A, K129A
Source method: isolated from a genetically manipulated source
Details: Cys188 is modified to CYSTEINESULFONIC ACID / Source: (gene. exp.) Homo sapiens (human) / Gene: NUDC / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y266

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Non-polymers , 2 types, 878 molecules

#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 877 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.35 Å3/Da / Density % sol: 47.55 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 25% PEG 3350, 0.2M sodium acetate, 0.1M lithium sulfate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.97928 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: May 5, 2005
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 1.75→28.05 Å / Num. all: 63806 / Num. obs: 63750 / % possible obs: 99.9 % / Observed criterion σ(F): 1.35 / Observed criterion σ(I): 1

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Processing

Software
NameVersionClassification
SERGUIdata collection
SHELXEmodel building
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.753→28.05 Å / SU ML: 0.22 / σ(F): 1.35 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2017 3227 5.06 %random
Rwork0.1727 ---
obs0.1742 63750 99.59 %-
all-63806 --
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.863 Å2 / ksol: 0.353 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.5261 Å2-0 Å20.2961 Å2
2---10.2632 Å2-0 Å2
3---7.7371 Å2
Refinement stepCycle: LAST / Resolution: 1.753→28.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4725 0 4 877 5606
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064998
X-RAY DIFFRACTIONf_angle_d1.0316818
X-RAY DIFFRACTIONf_dihedral_angle_d12.9341955
X-RAY DIFFRACTIONf_chiral_restr0.071763
X-RAY DIFFRACTIONf_plane_restr0.004875
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7527-1.81530.29713050.25655803X-RAY DIFFRACTION97
1.8153-1.8880.26623030.21156049X-RAY DIFFRACTION100
1.888-1.97390.24113230.18976040X-RAY DIFFRACTION100
1.9739-2.07790.20683200.17426051X-RAY DIFFRACTION100
2.0779-2.2080.21373310.17176037X-RAY DIFFRACTION100
2.208-2.37840.20993630.16626034X-RAY DIFFRACTION100
2.3784-2.61760.19593290.16396025X-RAY DIFFRACTION100
2.6176-2.9960.20932740.16486153X-RAY DIFFRACTION100
2.996-3.77320.17163430.16056100X-RAY DIFFRACTION100
3.7732-28.05680.18983360.17076231X-RAY DIFFRACTION100

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