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- PDB-5zbs: Crystal Structure of Kinesin-3 KIF13B motor Y73C mutant -

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Basic information

Entry
Database: PDB / ID: 5zbs
TitleCrystal Structure of Kinesin-3 KIF13B motor Y73C mutant
ComponentsKinesin family member 13BKinesin-like protein KIF13B
KeywordsTRANSPORT PROTEIN / Kinesin / ATPase
Function / homology
Function and homology information


Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / paranode region of axon / kinesin complex / microtubule motor activity / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding ...Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / cytoskeleton-dependent intracellular transport / paranode region of axon / kinesin complex / microtubule motor activity / regulation of axonogenesis / microtubule-based movement / microvillus / 14-3-3 protein binding / microtubule binding / microtubule / axon / protein kinase binding / ATP hydrolysis activity / ATP binding / cytosol / cytoplasm
Similarity search - Function
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-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 / 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
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Kinesin family member 13B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.203 Å
AuthorsRen, J.Q. / Wang, S. / Feng, W.
Funding support China, 6items
OrganizationGrant numberCountry
National Key R&D Program of China2017YFA0503501 China
National Major Basic Research Program of China2014CB910202 China
National Natural Science Foundation of China31470746 China
National Natural Science Foundation of China31770786 China
National Natural Science Foundation of China31600608 China
National Natural Science Foundation of China31600622 China
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structural Delineation of the Neck Linker of Kinesin-3 for Processive Movement.
Authors: Ren, J. / Zhang, Y. / Wang, S. / Huo, L. / Lou, J. / Feng, W.
History
DepositionFeb 12, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 22, 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_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.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.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Kinesin family member 13B
A: Kinesin family member 13B
C: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,18811
Polymers124,5483
Non-polymers1,6408
Water6,467359
1
B: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0463
Polymers41,5161
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15500 Å2
MethodPISA
2
A: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0714
Polymers41,5161
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-10 kcal/mol
Surface area15480 Å2
MethodPISA
3
C: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0714
Polymers41,5161
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)107.311, 107.311, 91.599
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Kinesin family member 13B / Kinesin-like protein KIF13B


Mass: 41515.898 Da / Num. of mol.: 3 / Fragment: the motor domain / Mutation: Y73C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kif13b / Plasmid: pET32a / Details (production host): C-terminal His tag / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0G2K8Z9
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.43 Å3/Da / Density % sol: 49.48 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 5.5 / Details: 0.1M Bis-Tris, 2.0M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 1 / Detector: CCD / Date: Jul 12, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 59423 / % possible obs: 99.6 % / Redundancy: 4.2 % / CC1/2: 0.998 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.2
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.678 / Mean I/σ(I) obs: 2.4 / CC1/2: 0.672 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.12_2829refinement
PHASERphasing
HKL-2000data collection
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GBJ

3gbj


Resolution: 2.203→41.44 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 0.17 / Phase error: 23.25
RfactorNum. reflection% reflection
Rfree0.2198 2824 5.01 %
Rwork0.1715 --
obs0.1739 56414 94.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 129.84 Å2 / Biso mean: 50.9247 Å2 / Biso min: 20.35 Å2
Refinement stepCycle: final / Resolution: 2.203→41.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7518 0 98 359 7975
Biso mean--39.87 50.26 -
Num. residues----986
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087724
X-RAY DIFFRACTIONf_angle_d0.97710455
X-RAY DIFFRACTIONf_chiral_restr0.0521215
X-RAY DIFFRACTIONf_plane_restr0.0061326
X-RAY DIFFRACTIONf_dihedral_angle_d5.9155832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Highest resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2031-2.24110.304136239284
2.2411-2.28180.303131239886
2.2818-2.32570.295156248588
2.3257-2.37320.2528145247489
2.3732-2.42480.2733140258891
2.4248-2.48120.2265144260092
2.4812-2.54320.2628128257092
2.5432-2.6120.2523130269893
2.612-2.68880.218113272095
2.6888-2.77560.2425162268796
2.7756-2.87480.2518147274297
2.8748-2.98980.2387129281598
2.9898-3.12590.20421390.1714279099
3.1259-3.29060.24511360.171283199
3.2906-3.49670.21211500.16492797100
3.4967-3.76650.21181500.15832816100
3.7665-4.14520.20331580.15762856100
4.1452-4.74430.17371350.1358276399
4.7443-5.97450.17691410.16472837100
5.97450.2315154273197
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)
10.7499-0.09340.62160.3124-0.28190.29310.0539-0.1619-0.1985-0.07480.01880.13040.182-0.122800.2508-0.0553-0.01560.33070.00970.3031-8.737955.299917.2216
20.9941-0.1076-0.0610.9169-0.38440.8120.02480.00430.0695-0.08880.0120.01660.0566-0.012800.2139-0.0042-0.01340.3039-0.02180.2402-7.84472.1271.4081
30.26950.4304-0.18560.7743-0.76211.3708-0.0476-0.02310.36340.0870.0184-0.0423-0.2585-0.001400.38630.01750.00930.3698-0.05730.4319-8.103287.64727.9663
41.4385-0.0556-0.81920.32090.40130.58110.0323-0.06660.20070.13510.06990.0912-0.3055-0.08110.00030.257-0.0103-0.02930.3393-0.00070.3232-13.5980.87611.8276
50.5258-0.5451-0.13430.72720.11690.50540.0778-0.34780.03950.2770.07460.1254-0.1273-0.40790.00010.32380.08130.04440.5207-0.06220.3564-23.60877.323120.7683
60.57230.0583-0.53710.8042-0.37530.36410.0076-0.07070.0040.05990.10060.2263-0.0947-0.331800.2332-0.0052-0.02240.4539-0.02520.3319-20.536870.49777.6987
70.5090.0827-0.01490.789-0.5431.07890.12370.15980.07380.06830.0570.1419-0.4038-0.37380.00190.39360.08250.05530.25090.02250.3128-55.1023104.155246.2637
80.45910.06480.19510.23210.23911.22030.01090.02490.0612-0.04820.02210.0238-0.0749-0.029500.27150.01450.01330.19470.01670.2613-41.232495.645129.369
90.3977-0.5256-0.10290.38420.06620.0394-0.0181-0.11670.0378-0.0496-0.1515-0.37580.03380.045-0.00030.3993-0.0358-0.03920.381-0.02380.472-23.233789.04842.7702
100.6755-0.20510.7790.1693-0.13680.91510.856-0.1277-0.06930.218-0.2538-0.06330.50730.07450.02880.41-0.03960.02080.3336-0.0760.4333-29.728186.960931.2958
111.25950.46210.77290.38280.25460.376-0.10270.15670.0648-0.0340.0262-0.0478-0.15220.2696-0.00010.33480.01110.04870.2880.0150.3709-29.624896.60826.167
120.8245-0.32690.8420.469-0.18470.6140.0469-0.32150.15820.3187-0.0081-0.0619-0.22230.31750.00110.4056-0.07530.02830.3178-0.06260.3438-30.2983104.765649.1168
130.8528-0.25720.41350.4220.29480.63380.0289-0.08680.26350.05670.0151-0.0869-0.32780.17170.00010.3606-0.04420.03960.18120.00340.3233-36.5447107.262737.2362
141.0674-0.0986-0.53720.9798-0.08931.52020.03410.18630.07230.0327-0.0508-0.0255-0.0499-0.068-00.32110.0009-0.01390.29860.04380.2951-45.686136.99434.0354
150.8827-0.474-0.17481.70960.62461.0603-0.04580.0192-0.0770.05470.0304-0.25230.04160.086400.36710.0328-0.0010.39930.06260.3796-28.647926.990629.4678
160.50380.2538-0.00630.9016-0.60320.8513-0.0183-0.01430.09590.2451-0.0339-0.2398-0.10360.3055-0.00010.3245-0.0732-0.04240.3260.00920.3471-30.972442.378636.8599
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 68 )B4 - 68
2X-RAY DIFFRACTION2chain 'B' and (resid 69 through 154 )B69 - 154
3X-RAY DIFFRACTION3chain 'B' and (resid 155 through 207 )B155 - 207
4X-RAY DIFFRACTION4chain 'B' and (resid 208 through 274 )B208 - 274
5X-RAY DIFFRACTION5chain 'B' and (resid 275 through 313 )B275 - 313
6X-RAY DIFFRACTION6chain 'B' and (resid 314 through 375 )B314 - 375
7X-RAY DIFFRACTION7chain 'A' and (resid 4 through 68 )A4 - 68
8X-RAY DIFFRACTION8chain 'A' and (resid 69 through 154 )A69 - 154
9X-RAY DIFFRACTION9chain 'A' and (resid 155 through 176 )A155 - 176
10X-RAY DIFFRACTION10chain 'A' and (resid 177 through 207 )A177 - 207
11X-RAY DIFFRACTION11chain 'A' and (resid 208 through 253 )A208 - 253
12X-RAY DIFFRACTION12chain 'A' and (resid 254 through 313 )A254 - 313
13X-RAY DIFFRACTION13chain 'A' and (resid 314 through 372 )A314 - 372
14X-RAY DIFFRACTION14chain 'C' and (resid 4 through 154 )C4 - 154
15X-RAY DIFFRACTION15chain 'C' and (resid 155 through 236 )C155 - 236
16X-RAY DIFFRACTION16chain 'C' and (resid 237 through 373 )C237 - 373

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