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- PDB-1t5c: Crystal structure of the motor domain of human kinetochore protei... -

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Basic information

Entry
Database: PDB / ID: 1t5c
TitleCrystal structure of the motor domain of human kinetochore protein CENP-E
ComponentsCentromeric protein E
KeywordsCONTRACTILE PROTEIN / kinesin motor-domain-ADP complex / stranded beta-sheet core with solvent exposed alpha-helices / arrow-head shape / Structural Proteomics in Europe / SPINE / Structural Genomics
Function / homology
Function and homology information


lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / mitotic chromosome movement towards spindle pole / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / kinetochore binding / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore ...lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / mitotic chromosome movement towards spindle pole / metaphase chromosome alignment / mitotic spindle midzone / kinetochore microtubule / kinetochore binding / kinetochore assembly / condensed chromosome, centromeric region / attachment of mitotic spindle microtubules to kinetochore / Kinesins / regulation of mitotic metaphase/anaphase transition / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / mitotic metaphase chromosome alignment / intercellular bridge / microtubule-based movement / chromosome, centromeric region / positive regulation of protein kinase activity / spindle midzone / 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 / MHC class II antigen presentation / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / mitotic spindle / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / chromosome / mitotic cell cycle / midbody / microtubule binding / microtubule / cell division / intracellular membrane-bounded organelle / ATP binding / membrane / nucleus / cytosol
Similarity search - Function
Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily ...Kinesin motor domain / Kinesin / Kinesin-like protein / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / NITRATE ION / Centromere-associated protein E
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsGarcia-Saez, I. / Yen, T. / Wade, R.H. / Kozielski, F. / Structural Proteomics in Europe (SPINE)
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of the motor domain of the human kinetochore protein CENP-E.
Authors: Garcia-Saez, I. / Yen, T. / Wade, R.H. / Kozielski, F.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Crystallization and preliminary crystallographic analysis of the motor domain of human kinetochore-associated protein CENP-E using an automated crystallization procedure.
Authors: Garcia-Saez, I. / Blot, D. / Kahn, R. / Kozielski, F.
History
DepositionMay 4, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 10, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Jun 17, 2020Group: Advisory / Database references / Polymer sequence
Category: entity_poly / pdbx_database_related ...entity_poly / pdbx_database_related / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_ref_seq_dif
Item: _entity_poly.pdbx_target_identifier / _struct_ref_seq_dif.details
Revision 2.1Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999SEQUENCE THE AUTHORS STATE, DNA SEQUENCING HAS SHOWN THE PRESENCE OF AN ALANINE IN POSITION 300 ...SEQUENCE THE AUTHORS STATE, DNA SEQUENCING HAS SHOWN THE PRESENCE OF AN ALANINE IN POSITION 300 INSTEAD OF A PROLINE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Centromeric protein E
B: Centromeric protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,9388
Polymers78,6712
Non-polymers1,2676
Water1,51384
1
A: Centromeric protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1515
Polymers39,3351
Non-polymers8164
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Centromeric protein E
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,7873
Polymers39,3351
Non-polymers4522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.353, 83.700, 94.162
Angle α, β, γ (deg.)90.00, 103.05, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Centromeric protein E / CENP-E protein


Mass: 39335.395 Da / Num. of mol.: 2 / Fragment: motor-domain and linker region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPE / Production host: Escherichia coli (E. coli) / References: UniProt: Q02224

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Non-polymers , 5 types, 90 molecules

#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NO3 / NITRATE ION


Mass: 62.005 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: NO3
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Chemical ChemComp-PIN / PIPERAZINE-N,N'-BIS(2-ETHANESULFONIC ACID) / PIPES / 1,4-PIPERAZINEDIETHANESULFONIC ACID


Mass: 302.368 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O6S2 / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.25 Å3/Da / Density % sol: 40 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 7
Details: PEG 3350, NaNO3, Pipes, pH 7.0, VAPOR DIFFUSION, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2003
RadiationMonochromator: Diamond (III), Ge (220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→91.73 Å / Num. all: 25698 / Num. obs: 25345 / % possible obs: 97.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 4.7 % / Rmerge(I) obs: 0.072 / Rsym value: 0.064 / Net I/σ(I): 6.4
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.182 / Mean I/σ(I) obs: 4.4 / Num. unique all: 3218 / Rsym value: 0.158 / % possible all: 86.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1.1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Structure of conventional kinesin motor domain PDB entry 1MKJ

1mkj


Resolution: 2.5→12 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.2782 1156 random
Rwork0.2277 --
all-24191 -
obs-23073 -
Refinement stepCycle: LAST / Resolution: 2.5→12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5055 0 78 84 5217
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg2.08
X-RAY DIFFRACTIONc_bond_d0.012
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.5-2.540.391260.305X-RAY DIFFRACTION686
3.02-3.10.23580.244X-RAY DIFFRACTION988
6.69-120.273580.23X-RAY DIFFRACTION1094

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