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- PDB-5jvp: The neck-linker and alpha 7 helix of Homo sapiens CENP-E -

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Basic information

Entry
Database: PDB / ID: 5jvp
TitleThe neck-linker and alpha 7 helix of Homo sapiens CENP-E
ComponentsChimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic chromosome movement towards spindle pole / mitotic spindle astral microtubule end / metaphase chromosome alignment / mitotic spindle midzone / protein localization to microtubule ...lateral attachment of mitotic spindle microtubules to kinetochore / microtubule plus-end directed mitotic chromosome migration / protein localization to astral microtubule / protein localization to mitotic spindle / cortical microtubule cytoskeleton / mitotic chromosome movement towards spindle pole / mitotic spindle astral microtubule end / metaphase chromosome alignment / mitotic spindle midzone / protein localization to microtubule / kinetochore binding / kinetochore microtubule / microtubule plus-end / cell projection membrane / mitotic spindle microtubule / kinetochore assembly / attachment of mitotic spindle microtubules to kinetochore / condensed chromosome, centromeric region / microtubule bundle formation / microtubule plus-end binding / non-motile cilium assembly / Kinesins / protein localization to centrosome / microtubule motor activity / regulation of mitotic metaphase/anaphase transition / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / mitotic metaphase chromosome alignment / mitotic spindle pole / negative regulation of microtubule polymerization / spindle midzone / microtubule polymerization / positive regulation of protein kinase activity / microtubule organizing center / establishment of mitotic spindle orientation / chromosome, centromeric region / regulation of microtubule polymerization or depolymerization / intercellular bridge / cytoplasmic microtubule / spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / positive regulation of microtubule polymerization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Mitotic Prometaphase / Recruitment of mitotic centrosome proteins and complexes / MHC class II antigen presentation / EML4 and NUDC in mitotic spindle formation / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / protein serine/threonine kinase binding / Resolution of Sister Chromatid Cohesion / AURKA Activation by TPX2 / mitotic spindle organization / chromosome segregation / RHO GTPases Activate Formins / kinetochore / The role of GTSE1 in G2/M progression after G2 checkpoint / mitotic spindle / Separation of Sister Chromatids / intracellular protein localization / Regulation of PLK1 Activity at G2/M Transition / cell migration / mitotic cell cycle / chromosome / microtubule cytoskeleton / midbody / microtubule binding / microtubule / ciliary basal body / cadherin binding / cell division / focal adhesion / intracellular membrane-bounded organelle / centrosome / Golgi apparatus / RNA binding / ATP binding / identical protein binding / nucleus / membrane / cytosol
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #1430 / EB1, C-terminal / Microtubule-associated protein RP/EB / EB1, C-terminal domain superfamily / EB1-C terminal (EB1-C) domain profile. / EB1-like C-terminal motif / Kinesin-like protein / Calponin homology (CH) domain / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Kinesin motor domain superfamily / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
: / Centromere-associated protein E / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.1 Å
AuthorsPhillips, R.K. / Rayment, I.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37-GM54141 United States
National Science Foundation (NSF, United States)DGE-0718123 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Family-specific Kinesin Structures Reveal Neck-linker Length Based on Initiation of the Coiled-coil.
Authors: Phillips, R.K. / Peter, L.G. / Gilbert, S.P. / Rayment, I.
History
DepositionMay 11, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2016Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2016Group: Database references
Revision 1.2Oct 5, 2016Group: Database references
Revision 1.3Sep 27, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 23, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
A: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
C: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
E: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
F: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,6269
Polymers64,2886
Non-polymers3373
Water8,755486
1
A: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules

A: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6544
Polymers21,4292
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area4470 Å2
ΔGint-40 kcal/mol
Surface area12520 Å2
MethodPISA
2
B: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules

B: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,6544
Polymers21,4292
Non-polymers2252
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_764-x+2,-x+y+1,-z-1/31
Buried area4340 Å2
ΔGint-42 kcal/mol
Surface area13410 Å2
MethodPISA
3
C: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,5423
Polymers21,4292
Non-polymers1121
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4430 Å2
ΔGint-39 kcal/mol
Surface area13090 Å2
MethodPISA
4
E: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1
F: Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)21,4292
Polymers21,4292
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4390 Å2
ΔGint-42 kcal/mol
Surface area12800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.609, 100.609, 107.627
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11D-101-

CD

21B-228-

HOH

31B-277-

HOH

41B-306-

HOH

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Components

#1: Protein
Chimera protein of Centromere-associated protein E and Microtubule-associated protein RP/EB family member 1 / Centromere protein E / CENP-E / Kinesin-related protein CENPE / APC-binding protein EB1 / End- ...Centromere protein E / CENP-E / Kinesin-related protein CENPE / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 10714.730 Da / Num. of mol.: 6
Fragment: UNP Q02224 residues 336-375,UNP Q15691 residues 210-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CENPE, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q02224, UniProt: Q15691
#2: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cd
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 486 / Source method: isolated from a natural source / Formula: H2O
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: 2.48 Å3/Da / Density % sol: 50.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 18% (w/v) MEPEG 2000, 175 mM Li2SO4, 100 mM MES pH 6.0, 1 mM CdCl2

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97929 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 9, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 2.1→45.786 Å / Num. obs: 71015 / % possible obs: 100 % / Redundancy: 16.6 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 16.6
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 12.7 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 2.1→45.785 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 28.4 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2739 3521 4.96 %
Rwork0.2372 --
obs0.239 71015 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→45.785 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 3 486 4814
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024372
X-RAY DIFFRACTIONf_angle_d0.4275858
X-RAY DIFFRACTIONf_dihedral_angle_d18.2362772
X-RAY DIFFRACTIONf_chiral_restr0.035659
X-RAY DIFFRACTIONf_plane_restr0.002771
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12880.28091370.26322651X-RAY DIFFRACTION99
2.1288-2.15920.32011460.27062676X-RAY DIFFRACTION100
2.1592-2.19150.32191420.2582715X-RAY DIFFRACTION100
2.1915-2.22570.32231480.26762733X-RAY DIFFRACTION100
2.2257-2.26220.35151400.25372660X-RAY DIFFRACTION100
2.2622-2.30120.35171400.27012742X-RAY DIFFRACTION100
2.3012-2.3430.28481360.25772654X-RAY DIFFRACTION100
2.343-2.38810.34091500.26012701X-RAY DIFFRACTION100
2.3881-2.43680.31431420.26592680X-RAY DIFFRACTION100
2.4368-2.48980.36551400.26242741X-RAY DIFFRACTION100
2.4898-2.54770.30641420.2482672X-RAY DIFFRACTION100
2.5477-2.61150.28731430.25492727X-RAY DIFFRACTION100
2.6115-2.68210.31441440.25062742X-RAY DIFFRACTION100
2.6821-2.7610.26791440.24362686X-RAY DIFFRACTION100
2.761-2.85010.38961360.24682683X-RAY DIFFRACTION100
2.8501-2.95190.2991290.2332714X-RAY DIFFRACTION100
2.9519-3.07010.28121440.23882685X-RAY DIFFRACTION100
3.0701-3.20980.27411360.24022717X-RAY DIFFRACTION100
3.2098-3.37890.25481460.22752707X-RAY DIFFRACTION100
3.3789-3.59060.30211420.23732730X-RAY DIFFRACTION100
3.5906-3.86770.22761350.22372703X-RAY DIFFRACTION100
3.8677-4.25660.19461420.19562691X-RAY DIFFRACTION100
4.2566-4.8720.22741380.1942700X-RAY DIFFRACTION100
4.872-6.13590.23061380.24632701X-RAY DIFFRACTION100
6.1359-45.79580.22331410.22842683X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.61071.2013-0.07311.7014-0.30550.64410.2783-0.0959-0.09080.1073-0.1353-0.1272-0.05690.0798-0.04750.0959-0.03950.0990.1167-0.02590.066942.080675.35551.2643
24.92021.2306-0.24780.80330.71491.85780.2062-0.0213-0.6285-0.2309-0.0760.16050.2147-0.0738-0.0580.41450.0392-0.19590.1181-0.11450.545529.762543.042-7.9287
31.7884-1.94380.22533.6728-0.33780.3426-0.0335-0.01460.07410.10840.0506-0.0904-0.0387-0.0594-0.00530.16050.01720.07980.03950.03280.056553.271979.6774-16.363
40.62140.11340.17940.93520.05161.4166-0.0620.0742-0.5111-0.00790.0585-0.10510.36330.3223-0.05120.21660.14440.13770.2353-0.08110.442576.920250.6532-24.9942
54.31140.3128-1.31430.1347-0.15540.4739-0.131-0.41090.155-0.070.0083-0.0039-0.05430.1003-0.03230.20420.05110.01330.2796-0.12820.099438.437929.872319.0178
60.35620.10270.28631.15660.13621.70750.0142-0.1870.0678-0.0758-0.10460.36290.1152-0.56930.57520.346-0.193-0.04640.5626-0.29820.45560.567421.294911.5195
72.6069-0.9647-1.99271.21880.9161.56020.24330.2044-0.2902-0.2685-0.21420.26670.0404-0.35560.00730.18220.0557-0.09770.39480.09280.235872.510428.511630.4914
84.27111.32511.46050.60270.20550.7578-0.21380.6674-0.408-0.15070.086-0.0619-0.13690.08340.05070.25960.021-0.02080.2331-0.04790.076433.827127.047715.1007
93.91080.5489-0.97462.66711.31683.33020.15190.27380.1219-0.0492-0.25420.4029-0.1103-0.63950.27870.31920.16490.01390.399-0.17550.25232.992530.645926.1679
102.85212.94211.12783.68931.31220.4638-0.45070.2091-0.0674-0.35630.2422-0.0366-0.0328-0.0463-0.00780.3871-0.07840.08390.2921-0.08620.1571-3.810849.8267-1.459
111.49151.0758-0.98911.5129-0.1171.7818-0.36260.0796-0.6816-0.285-0.0357-0.25370.6578-0.01970.4320.6865-0.1770.42520.4624-0.13950.6816-29.027223.34556.7832
120.96941.518-0.39742.4655-0.59590.12580.1355-0.2049-0.08390.3445-0.3252-0.10470.03860.0248-0.03660.4668-0.1270.15150.3272-0.01320.235-5.391851.78781.3086
130.9636-0.01780.12840.4428-0.7131.64990.1285-0.06280.07780.22720.1528-0.02120.49730.1060.51910.6799-0.03650.2180.4115-0.22620.5268-21.057319.5692-8.3682
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 63 )
2X-RAY DIFFRACTION2chain 'A' and (resid 64 through 90 )
3X-RAY DIFFRACTION3chain 'B' and (resid 1 through 63 )
4X-RAY DIFFRACTION4chain 'B' and (resid 64 through 90 )
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 62 )
6X-RAY DIFFRACTION6chain 'C' and (resid 63 through 90 )
7X-RAY DIFFRACTION7chain 'D' and (resid 1 through 7 )
8X-RAY DIFFRACTION8chain 'D' and (resid 8 through 64 )
9X-RAY DIFFRACTION9chain 'D' and (resid 65 through 90 )
10X-RAY DIFFRACTION10chain 'E' and (resid 1 through 63 )
11X-RAY DIFFRACTION11chain 'E' and (resid 64 through 90 )
12X-RAY DIFFRACTION12chain 'F' and (resid 1 through 62 )
13X-RAY DIFFRACTION13chain 'F' and (resid 63 through 89 )

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