[English] 日本語
Yorodumi
- PDB-2gry: Crystal structure of the human KIF2 motor domain in complex with ADP -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2gry
TitleCrystal structure of the human KIF2 motor domain in complex with ADP
ComponentsKinesin-like protein KIF2
KeywordsTRANSPORT PROTEIN / kinesin / motor domain / adp / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC
Function / homology
Function and homology information


centriolar subdistal appendage / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / microtubule motor activity / microtubule-based movement / cytoskeletal motor activity / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal ...centriolar subdistal appendage / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule depolymerization / kinesin complex / microtubule motor activity / microtubule-based movement / cytoskeletal motor activity / mitotic spindle assembly / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Mitotic Prometaphase / regulation of cell migration / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / centriole / mitotic spindle organization / RHO GTPases Activate Formins / spindle / microtubule cytoskeleton organization / spindle pole / Separation of Sister Chromatids / nervous system development / microtubule binding / microtubule / cell differentiation / nuclear body / cell division / centrosome / nucleolus / ATP hydrolysis activity / nucleoplasm / ATP binding / membrane / cytosol / cytoplasm
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 / : / Kinesin-like protein KIF2A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
AuthorsWang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: to be published
Title: Crystal structure of the human KIF2 motor domain in complex with ADP
Authors: Wang, J. / Shen, Y. / Tempel, W. / Landry, R. / Arrowsmith, C.H. / Edwards, A.M. / Sundstrom, M. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionApr 25, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Aug 30, 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 / 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 / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN. THE BIOLOGICAL UNIT OF THIS PROTEIN IS UNKNOWN.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Kinesin-like protein KIF2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3706
Polymers47,9191
Non-polymers4525
Water45025
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.475, 121.475, 175.684
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

-
Components

#1: Protein Kinesin-like protein KIF2 / Kinesin-2 / HK2


Mass: 47918.902 Da / Num. of mol.: 1 / Fragment: KIF2 motor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF2, KNS2 / Plasmid: p28a-LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus (DE-3)-RIL / References: GenBank: 21594340, UniProt: O00139*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-UNX / UNKNOWN ATOM OR ION


Num. of mol.: 3 / Source method: obtained synthetically
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 3.5M sodium formate, 0.1M sodium acetate, pH 4.6, vapor diffusion, sitting drop, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Apr 18, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.35→30 Å / Num. obs: 21011 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.068 / Χ2: 1.144 / Net I/σ(I): 12.1
Reflection shell
Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID
2.35-2.431007.90.9520800.9661
2.43-2.5310080.7420980.9621
2.53-2.651008.10.58520460.9921
2.65-2.791008.10.38620761.0471
2.79-2.961008.10.24720971.091
2.96-3.191008.10.14320901.1481
3.19-3.511008.10.08120931.2451
3.51-4.021008.10.05320981.4281
4.02-5.061008.20.03721301.3991
5.06-301007.90.02522031.1441

-
Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å29.48 Å
Translation2.5 Å29.48 Å

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefmac_5.2.0019refinement
PDB_EXTRACT1.701data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1V8K

1v8k


Resolution: 2.35→29.285 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.893 / WRfactor Rfree: 0.279 / WRfactor Rwork: 0.212 / SU B: 14.685 / SU ML: 0.17 / TLS residual ADP flag: LIKELY RESIDUAL / ESU R: 0.275 / ESU R Free: 0.244 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2833 1077 5.137 %random
Rwork0.2215 ---
all0.224 ---
obs-20965 99.795 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 57.036 Å2
Baniso -1Baniso -2Baniso -3
1-0.297 Å20.149 Å20 Å2
2--0.297 Å20 Å2
3----0.446 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.285 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2516 0 31 25 2572
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222587
X-RAY DIFFRACTIONr_angle_refined_deg1.3941.9793495
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4195324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.45522.778108
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.67315448
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2811523
X-RAY DIFFRACTIONr_chiral_restr0.090.2406
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021897
X-RAY DIFFRACTIONr_nbd_refined0.2010.21102
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21728
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.298
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1150.22
X-RAY DIFFRACTIONr_mcbond_it2.46721688
X-RAY DIFFRACTIONr_mcangle_it3.51832611
X-RAY DIFFRACTIONr_scbond_it2.81421022
X-RAY DIFFRACTIONr_scangle_it3.8623883
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection all% reflection obs (%)
2.35-2.4110.355730.25814660.262154199.87
2.411-2.4760.303750.23914020.243147899.932
2.476-2.5480.303670.2513780.253144999.724
2.548-2.6250.25960.23813080.239140799.787
2.625-2.7110.287690.24112900.244136099.926
2.711-2.8050.264810.22512330.2281314100
2.805-2.910.321790.21412060.221128899.767
2.91-3.0280.308610.22311700.227123399.838
3.028-3.1610.31540.21911240.223118099.831
3.161-3.3130.219620.2310650.229113099.735
3.313-3.490.221590.20810210.209109099.083
3.49-3.6980.209470.1939730.194102599.512
3.698-3.9490.243550.1969060.19896699.482
3.949-4.2590.276390.1868600.1990199.778
4.259-4.6560.234350.1858040.187839100
4.656-5.1890.216300.1947310.195761100
5.189-5.960.334380.2546460.258684100
5.96-7.2250.453240.3015650.306589100
7.225-9.9210.33140.2254550.228469100
9.921-29.2850.433190.3042850.313304100
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)
11.57630.44090.32562.04950.29992.2317-0.0084-0.04660.1486-0.0625-0.14640.2995-0.2207-0.11390.1549-0.26250.019-0.0104-0.287-0.1238-0.226926.809-17.66726.483
24.7492-9.99375.836628.4363-2.13621.07220.43461.0634-0.0347-2.8463-2.49872.0907-1.4136-0.88992.064-0.0223-0.0013-0.06480.0084-0.0914-0.013433.605-12.85715.063
316.6922-2.9878-3.26318.35591.02092.80570.17480.7141.1778-0.7353-0.2096-0.1683-0.2989-0.97220.03470.61130.0349-0.17660.4566-0.04960.437218.085-18.026-1.391
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A

IDRefine TLS-IDLabel asym-IDAuth seq-IDLabel seq-ID
11A191 - 52385 - 417
22C6011
33A169 - 18663 - 80

+
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://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