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- PDB-3gbj: Crystal structure of the motor domain of kinesin KIF13B bound with ADP -

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Basic information

Entry
Database: PDB / ID: 3gbj
TitleCrystal structure of the motor domain of kinesin KIF13B bound with ADP
ComponentsKIF13B protein
KeywordsMOTOR PROTEIN / kinesin / motor domain / ADP / STRUCTURAL GENOMICS / STRUCTURAL GENOMICS CONSORTIUM / SGC / ATP-binding / Microtubule / Nucleotide-binding
Function / homology
Function and homology information


plus-end-directed vesicle transport along microtubule / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / regulation of axonogenesis / microtubule-based movement / protein targeting / 14-3-3 protein binding ...plus-end-directed vesicle transport along microtubule / cytoskeleton-dependent intracellular transport / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / regulation of axonogenesis / microtubule-based movement / protein targeting / 14-3-3 protein binding / T cell activation / microtubule binding / microtubule / axon / protein kinase binding / signal transduction / ATP hydrolysis activity / ATP binding / cytoplasm
Similarity search - Function
Kinesin-like protein KIF13A / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. ...Kinesin-like protein KIF13A / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / Kinesin-associated / Kinesin-associated / Kinesin motor domain / Kinesin / Kinesin-like protein / FHA domain / Forkhead-associated (FHA) 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 / SMAD/FHA domain superfamily / 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 / Kinesin-like protein KIF13B
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.102 Å
AuthorsTong, Y. / Shen, L. / Shen, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H. / Structural Genomics Consortium (SGC)
CitationJournal: To be Published
Title: Crystal structure of the motor domain of kinesin KIF13B bound with ADP
Authors: Tong, Y. / Shen, L. / Shen, Y. / Tempel, W. / Arrowsmith, C.H. / Edwards, A.M. / Bountra, C. / Weigelt, J. / Bochkarev, A. / Park, H.
History
DepositionFeb 19, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 3, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Sep 6, 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_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_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_asym_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_ref_seq_dif.details / _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: KIF13B protein
B: KIF13B protein
C: KIF13B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,68214
Polymers117,3273
Non-polymers1,35511
Water2,450136
1
A: KIF13B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5615
Polymers39,1091
Non-polymers4524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: KIF13B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5615
Polymers39,1091
Non-polymers4524
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: KIF13B protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5614
Polymers39,1091
Non-polymers4523
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.229, 86.520, 94.948
Angle α, β, γ (deg.)90.000, 106.800, 90.000
Int Tables number4
Space group name H-MP1211
DetailsAUTHORS STATE THAT THE BIOLOGICAL UNIT IS UNKNOWN AT THE TIME OF DEPOSITION

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Components

#1: Protein KIF13B protein


Mass: 39109.121 Da / Num. of mol.: 3 / Fragment: UNP residues 4-351
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF13B / Plasmid: pET28a-LIC-CHis / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3-V2R pRARE2 / References: UniProt: A0JLQ2, UniProt: Q9NQT8*PLUS
#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 3 / 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.: 3 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-UNX / UNKNOWN ATOM OR ION


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


Mass: 18.015 Da / Num. of mol.: 136 / Source method: isolated from a natural source / Formula: H2O

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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: 2.49 Å3/Da / Density % sol: 50.56 %
Description: The structure factor file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 3350, Ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97937 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 15, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97937 Å / Relative weight: 1
ReflectionResolution: 2.1→40 Å / Num. obs: 133690 / % possible obs: 99.9 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.065 / Χ2: 1.356 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.1-2.143.70.94733131.394100
2.14-2.183.70.80833331.367100
2.18-2.223.70.70733251.396100
2.22-2.263.70.60533162.05799.9
2.26-2.313.70.6233431.436100
2.31-2.373.80.4533171.364100
2.37-2.423.70.39933421.354100
2.42-2.493.80.34533361.372100
2.49-2.563.80.26533481.308100
2.56-2.653.80.20733121.315100
2.65-2.743.80.18133291.299100
2.74-2.853.80.12933751.26100
2.85-2.983.80.09433111.183100
2.98-3.143.80.07333431.158100
3.14-3.333.80.05133351.106100
3.33-3.593.70.04233541.158100
3.59-3.953.70.04233581.60999.9
3.95-4.523.70.03933681.87100
4.52-5.73.60.02833931.22699.9
5.7-403.70.02133910.90798.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
HKL-3000data reduction
HKL-3000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1I6I

1i6i


Resolution: 2.102→39.062 Å / FOM work R set: 0.797 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: The Friedel pairs were used in phasing. Programs coot, molprobity have also been used in refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.269 3474 2.67 %Thin shells
Rwork0.221 ---
obs0.222 133690 98.93 %-
Solvent computationShrinkage radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.55 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso max: 162.21 Å2 / Biso mean: 46.3 Å2 / Biso min: 15.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.877 Å2-0 Å2-2.799 Å2
2--2.964 Å2-0 Å2
3----2.087 Å2
Refinement stepCycle: LAST / Resolution: 2.102→39.062 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6531 0 89 136 6756
Refinement TLS params.

S33: -0 Å ° / 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 °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.75780.2871-0.35440.6933-0.58730.86530.0450.13240.0784-0.01530.04350.043-0.0893-0.14870.33880.0366-0.00060.28450.04160.2186-23.6571-18.6667-1.7065
20.6762-0.6416-0.23890.91340.40630.68360.0728-0.08490.0441-0.06290.0232-0.05660.00850.0770.1629-0.01290.01960.1697-0.01250.2076-11.8153-37.702334.3616
31.02830.45580.76821.02640.67721.28010.1294-0.0192-0.11120.17460.09730.00540.1924-0.02650.17370.0131-0.04450.17470.01090.213-19.471-48.3335-32.644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C

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