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- PDB-4a14: HUMAN KIF7, A KINESIN INVOLVED IN HEDGEHOG SIGNALLING -

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Basic information

Entry
Database: PDB / ID: 4a14
TitleHUMAN KIF7, A KINESIN INVOLVED IN HEDGEHOG SIGNALLING
ComponentsKINESIN-LIKE PROTEIN KIF7
KeywordsMOTOR PROTEIN / KINESIN / MOTOR DOMAIN
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: 1.6 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
DepositionSep 14, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2012Group: Other
Revision 1.2Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KINESIN-LIKE PROTEIN KIF7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,8983
Polymers37,4461
Non-polymers4522
Water5,909328
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)45.991, 79.799, 95.094
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein KINESIN-LIKE PROTEIN KIF7 / KINESIN


Mass: 37446.348 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 8-347
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.: 328 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsRESIDUES 1,2,3, AND 4 - CHANGES OWING TO CLONING STRATEGY.

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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: 2.33 Å3/Da / Density % sol: 47.34 % / Description: NONE
Crystal growDetails: 20% POLYETHYLENE GLYCOL 3350, 0.20 M LITHIUM ACETATE.

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.9173
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jul 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9173 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 46998 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 7.5 % / Biso Wilson estimate: 22.26 Å2 / Rmerge(I) obs: 0.03 / Net I/σ(I): 30.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 7.5 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 4.4 / % possible all: 100

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Processing

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

3b6v


Resolution: 1.6→29.459 Å / SU ML: 0.42 / σ(F): 1.34 / Phase error: 19.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2067 2374 5.1 %
Rwork0.1825 --
obs0.1837 46930 99.91 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.797 Å2 / ksol: 0.329 e/Å3
Displacement parametersBiso mean: 29.09 Å2
Baniso -1Baniso -2Baniso -3
1-4.8603 Å20 Å20 Å2
2---5.2824 Å20 Å2
3---0.4221 Å2
Refinement stepCycle: LAST / Resolution: 1.6→29.459 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2241 0 28 328 2597
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112435
X-RAY DIFFRACTIONf_angle_d1.5473327
X-RAY DIFFRACTIONf_dihedral_angle_d15.046910
X-RAY DIFFRACTIONf_chiral_restr0.115386
X-RAY DIFFRACTIONf_plane_restr0.008435
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6-1.63270.31631490.2842589X-RAY DIFFRACTION100
1.6327-1.66820.27671350.24632557X-RAY DIFFRACTION100
1.6682-1.7070.27491470.25582592X-RAY DIFFRACTION100
1.707-1.74970.29891490.26122544X-RAY DIFFRACTION100
1.7497-1.7970.31061140.23272622X-RAY DIFFRACTION100
1.797-1.84980.23151280.20462617X-RAY DIFFRACTION100
1.8498-1.90950.22071290.19152605X-RAY DIFFRACTION100
1.9095-1.97770.23181430.18292567X-RAY DIFFRACTION100
1.9777-2.05690.2091460.17922589X-RAY DIFFRACTION100
2.0569-2.15050.221390.18292610X-RAY DIFFRACTION100
2.1505-2.26380.20041600.1732590X-RAY DIFFRACTION100
2.2638-2.40560.19871410.17642635X-RAY DIFFRACTION100
2.4056-2.59130.19981540.17612615X-RAY DIFFRACTION100
2.5913-2.85180.21171130.17772655X-RAY DIFFRACTION100
2.8518-3.2640.20011370.17282662X-RAY DIFFRACTION100
3.264-4.11060.17221330.15972686X-RAY DIFFRACTION100
4.1106-29.4640.1961570.18282821X-RAY DIFFRACTION100
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)
12.0435-0.69761.13192.3758-1.7612.90910.0022-0.06380.16310.3012-0.013-0.2473-0.23130.0239-0.02610.29110.0089-0.06960.1601-0.02720.1568-15.942116.5898-7.9672
22.27691.00211.10013.09932.09394.13120.0848-0.14470.17430.3689-0.17110.4185-0.3471-0.48770.14740.28190.0450.03170.2337-0.03820.221-30.58818.3303-11.0232
32.71530.9490.66422.10540.73870.73820.0871-0.0880.01480.3347-0.13950.1607-0.0635-0.15830.01560.16440.0306-0.01220.1773-0.03350.1577-30.72390.7459-15.3945
42.45931.3111-0.40562.83310.29912.3533-0.0883-0.0279-0.40510.20220.0327-0.51920.40910.34820.10950.18940.0644-0.05180.1726-0.01190.2131-18.7388-13.4546-21.378
53.33750.5215-2.50443.1031-0.49426.186-0.10430.19940.005-0.14860.03340.02970.2128-0.3245-0.01640.1210.0087-0.02380.1663-0.03130.1447-26.9204-10.8313-27.4332
62.1070.11251.41495.6697-0.70895.06760.3102-0.436-0.40751.0184-0.0903-0.74910.46330.212-0.04560.49490.0248-0.1510.2225-0.0190.2351-22.6715-12.9558-9.6127
76.48760.73472.46284.22360.44793.74970.00330.2037-0.18270.4-0.0264-0.0595-0.0199-0.0634-0.05330.12690.0218-0.03910.1182-0.01630.1197-26.1371-6.0586-21.1369
83.2874-0.14650.85261.48770.30031.9501-0.10930.05550.1250.0470.1002-0.3021-0.08060.0701-0.01980.13010.0185-0.04320.1281-0.02230.1913-16.8408-0.1012-21.3839
93.2704-1.98391.11776.24170.07492.30950.04340.3310.1758-0.683-0.0381-0.3916-0.26570.3186-0.01250.2194-0.02270.05230.2386-0.03580.234-13.5596.8718-30.4998
100.61720.5479-0.77432.82350.95410.80760.05730.0148-0.04290.0130.0887-0.2738-0.10950.0492-0.12190.1480.0196-0.04110.1638-0.01820.1666-14.54989.3932-17.5217
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 9:60)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 61:76)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 77:135)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 136:165)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 166:186)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 187:210)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 211:239)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 240:275)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 276:304)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 305:344)

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