[English] 日本語
Yorodumi
- PDB-5jv3: The neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5jv3
TitleThe neck-linker and alpha 7 helix of Homo sapiens Eg5 fused to EB1
ComponentsChimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
KeywordsMOTOR PROTEIN / kinesin / coiled-coil
Function / homology
Function and homology information


protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / spindle elongation / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / non-motile cilium assembly / microtubule bundle formation ...protein localization to astral microtubule / cortical microtubule cytoskeleton / mitotic spindle astral microtubule end / protein localization to microtubule / spindle elongation / microtubule plus-end / cell projection membrane / attachment of mitotic spindle microtubules to kinetochore / non-motile cilium assembly / microtubule bundle formation / microtubule plus-end binding / regulation of mitotic centrosome separation / Kinesins / plus-end-directed microtubule motor activity / mitotic centrosome separation / protein localization to centrosome / COPI-dependent Golgi-to-ER retrograde traffic / microtubule organizing center / microtubule motor activity / negative regulation of microtubule polymerization / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle pole / microtubule polymerization / cytoplasmic microtubule / establishment of mitotic spindle orientation / mitotic spindle assembly / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / AURKA Activation by TPX2 / mitotic spindle organization / ciliary basal body / RHO GTPases Activate Formins / protein localization / spindle microtubule / mitotic spindle / spindle pole / spindle / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Regulation of PLK1 Activity at G2/M Transition / cell migration / mitotic cell cycle / microtubule binding / microtubule / cadherin binding / cell division / focal adhesion / centrosome / protein kinase binding / Golgi apparatus / protein-containing complex / RNA binding / ATP binding / identical protein binding / membrane / nucleus / 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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : ...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-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / 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
Kinesin-like protein KIF11 / Microtubule-associated protein RP/EB family member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.006 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)R37-GM54141 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 10, 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 1.5Sep 27, 2023Group: Data collection / Database references ...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 / struct_conn
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_asym_id / _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.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_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_asym_id / _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_symmetry

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
C: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8615
Polymers35,8214
Non-polymers401
Water4,684260
1
A: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
B: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1


Theoretical massNumber of molelcules
Total (without water)17,9102
Polymers17,9102
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-40 kcal/mol
Surface area9630 Å2
MethodPISA
2
C: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
D: Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9503
Polymers17,9102
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-36 kcal/mol
Surface area9740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.839, 59.502, 72.664
Angle α, β, γ (deg.)90.00, 100.58, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Chimera protein of Kinesin-like protein KIF11 and Microtubule-associated protein RP/EB family member 1 / Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / ...Kinesin-like protein 1 / Kinesin-like spindle protein HKSP / Kinesin-related motor protein Eg5 / Thyroid receptor-interacting protein 5 / TRIP-5 / APC-binding protein EB1 / End-binding protein 1 / EB1


Mass: 8955.164 Da / Num. of mol.: 4
Fragment: UNP P52732 residues 366-391,UNP Q15691 residues 210-257
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF11, EG5, KNSL1, TRIP5, MAPRE1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P52732, UniProt: Q15691
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 260 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.04 Å3/Da / Density % sol: 39.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 24% (w/v) PEE797, 100 mM CaCl2, 100 mM MOPS pH 7.0, 0.1% (w/v) octylglucoside

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2→30.622 Å / Num. obs: 19131 / % possible obs: 97 % / Redundancy: 4.1 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 25.9
Reflection shellResolution: 2→2.09 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 3.8 / % possible all: 99.9

-
Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1YIB

1yib


Resolution: 2.006→30.622 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 962 5.03 %
Rwork0.2154 --
obs0.217 19131 97.07 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.006→30.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2205 0 1 260 2466
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022239
X-RAY DIFFRACTIONf_angle_d0.3242998
X-RAY DIFFRACTIONf_dihedral_angle_d17.4431410
X-RAY DIFFRACTIONf_chiral_restr0.032333
X-RAY DIFFRACTIONf_plane_restr0.002391
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0056-2.11140.30541250.26162283X-RAY DIFFRACTION86
2.1114-2.24360.27591380.23352609X-RAY DIFFRACTION99
2.2436-2.41680.26351390.22972685X-RAY DIFFRACTION100
2.4168-2.65990.25091410.23192658X-RAY DIFFRACTION100
2.6599-3.04440.29151420.22552659X-RAY DIFFRACTION100
3.0444-3.83450.23411420.19612694X-RAY DIFFRACTION100
3.8345-30.62560.21061350.20172581X-RAY DIFFRACTION95
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)
11.878-0.1678-2.02472.70892.5348.45930.0757-0.30760.00570.65070.00190.1850.34920.1061-0.00760.2607-0.03780.00630.1286-0.00330.315214.4565-0.556547.9225
24.5895-1.9383-0.66756.1311.92655.04180.53540.5810.1968-1.19240.03270.7843-0.4128-0.9943-0.1220.37660.0254-0.18740.41870.20220.547810.7813-2.194120.6591
33.1223-3.19990.14713.3585-0.12350.01660.526-0.22540.5828-1.0643-0.284-0.0258-0.08370.4116-0.57990.8266-0.02690.25480.7498-0.04090.50030.79717.24968.8619
42.4927-0.8523-2.17354.00932.54258.92440.007-0.0402-0.12740.2324-0.13680.43270.0024-0.43350.19160.0768-0.0337-0.04570.11250.00750.30669.9803-5.583639.1458
58.6341-1.5243.06057.1743-4.80437.7242-0.14790.2176-0.1594-0.11530.0332-0.6178-0.15750.18550.07590.12520.0257-0.00280.1218-0.06090.314625.9687-10.125329.8788
65.587-7.11476.23832.0015-8.0037.01530.96410.4811-0.35270.6970.0972-2.2110.75353.0169-0.89910.50990.0259-0.26330.9206-0.2130.63956.2988-20.63348.1467
70.64830.551-1.13520.7912-0.21224.2057-0.04860.31850.024-0.63260.0607-0.1052-0.4608-0.6691-0.0180.57860.10230.03230.322-0.01230.17650.5088-16.12897.2436
86.5225-5.68946.56945.7707-5.6426.6232-0.7996-1.18060.18440.44390.67840.7173-1.396-2.3992-0.20910.54380.25810.00630.70180.03050.3621-12.9805-14.849442.6131
90.93530.3207-1.42120.6245-0.40596.1973-0.03740.16320.0381-0.70130.1104-0.00350.5075-0.0238-0.03630.56760.06520.05210.2084-0.02030.172.6067-21.199212.348
107.2995-0.1604-4.35792.0749-0.02963.483-0.47170.9510.161-0.09720.1745-0.2253-1.78830.14210.23031.0332-0.150.04070.46360.03040.29417.1455-9.9373-10.0099
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 8 through 49 )
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 72 )
3X-RAY DIFFRACTION3chain 'B' and (resid 8 through 15 )
4X-RAY DIFFRACTION4chain 'B' and (resid 16 through 53 )
5X-RAY DIFFRACTION5chain 'B' and (resid 54 through 76 )
6X-RAY DIFFRACTION6chain 'C' and (resid 3 through 7 )
7X-RAY DIFFRACTION7chain 'C' and (resid 8 through 66 )
8X-RAY DIFFRACTION8chain 'D' and (resid 1 through 7 )
9X-RAY DIFFRACTION9chain 'D' and (resid 8 through 53 )
10X-RAY DIFFRACTION10chain 'D' and (resid 54 through 68 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more