[English] 日本語
Yorodumi
- PDB-2xt3: HUMAN KIF7, A KINESIN INVOLVED IN HEDGEHOG SIGNALLING -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xt3
TitleHUMAN KIF7, A KINESIN INVOLVED IN HEDGEHOG SIGNALLING
ComponentsKINESIN-LIKE PROTEIN KIF7
KeywordsMOTOR PROTEIN / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


ciliary tip / positive regulation of smoothened signaling pathway / kinesin complex / microtubule motor activity / microtubule-based movement / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / ciliary basal body / Hedgehog 'on' state / cilium ...ciliary tip / positive regulation of smoothened signaling pathway / kinesin complex / microtubule motor activity / microtubule-based movement / Hedgehog 'off' state / negative regulation of smoothened signaling pathway / ciliary basal body / Hedgehog 'on' state / cilium / microtubule binding / microtubule / ATP hydrolysis activity / ATP binding / 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 KIF7
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.882 Å
AuthorsKlejnot, M. / Kozielski, F.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural Insights Into Human Kif7, a Kinesin Involved in Hedgehog Signalling.
Authors: Klejnot, M. / Kozielski, F.
History
DepositionOct 4, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 25, 2012Group: Other
Revision 1.2Feb 15, 2012Group: Other
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KIF7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8743
Polymers37,4221
Non-polymers4522
Water5,224290
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.920, 79.790, 94.840
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein KINESIN-LIKE PROTEIN KIF7 / KINESIN


Mass: 37422.371 Da / Num. of mol.: 1 / Fragment: RESIDUES 7-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PETM20MOD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): CODONPLUS-RIPL / References: UniProt: Q2M1P5
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 290 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 226 TO LYS ENGINEERED RESIDUE IN CHAIN A, ARG 268 TO LEU ...ENGINEERED RESIDUE IN CHAIN A, GLU 226 TO LYS ENGINEERED RESIDUE IN CHAIN A, ARG 268 TO LEU ENGINEERED RESIDUE IN CHAIN A, LEU 269 TO ARG ENGINEERED RESIDUE IN CHAIN A, HIS 298 TO ASN
Sequence detailsRESIDUES 1-7 CONTAIN CHANGES DUE TO CLONING STRATEGY MUTATIONS 226 E TO K, 268 R TO L, 269 L TO R, 298 H TO N.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.13 % / Description: NONE
Crystal growpH: 6 / Details: pH 6.0

-
Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 14, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.88→30 Å / Num. obs: 28661 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 5.7 % / Biso Wilson estimate: 21.5 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.1
Reflection shellResolution: 1.88→1.98 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 6.1 / % possible all: 100

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
iMOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3B6V

3b6v


Resolution: 1.882→28.704 Å / SU ML: 0.2 / σ(F): 0 / Phase error: 21.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2291 1440 5.1 %
Rwork0.1791 --
obs0.1816 28342 97.82 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 58.861 Å2 / ksol: 0.402 e/Å3
Displacement parametersBiso mean: 23.779 Å2
Baniso -1Baniso -2Baniso -3
1-4.0143 Å20 Å20 Å2
2---4.9806 Å20 Å2
3---0.9662 Å2
Refinement stepCycle: LAST / Resolution: 1.882→28.704 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 28 290 2571
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012362
X-RAY DIFFRACTIONf_angle_d1.4583213
X-RAY DIFFRACTIONf_dihedral_angle_d15.117857
X-RAY DIFFRACTIONf_chiral_restr0.11377
X-RAY DIFFRACTIONf_plane_restr0.006417
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.882-1.94930.31251470.23322579X-RAY DIFFRACTION96
1.9493-2.02730.27081500.20972630X-RAY DIFFRACTION98
2.0273-2.11950.26651450.19052659X-RAY DIFFRACTION99
2.1195-2.23120.22371350.17892704X-RAY DIFFRACTION99
2.2312-2.3710.25191460.17752696X-RAY DIFFRACTION99
2.371-2.55390.22971530.192713X-RAY DIFFRACTION99
2.5539-2.81070.251400.18672733X-RAY DIFFRACTION99
2.8107-3.2170.25291390.17832738X-RAY DIFFRACTION99
3.217-4.05120.19511480.15222738X-RAY DIFFRACTION98
4.0512-28.70730.19491370.17822712X-RAY DIFFRACTION93

+
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