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- PDB-5zbr: Crystal Structure of Kinesin-3 KIF13B motor domain in AMPPNP form -

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Basic information

Entry
Database: PDB / ID: 5zbr
TitleCrystal Structure of Kinesin-3 KIF13B motor domain in AMPPNP form
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 / PHOSPHATE ION / Kinesin family member 13B
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_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

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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)126,65314
Polymers124,7283
Non-polymers1,92511
Water9,908550
1
B: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,3216
Polymers41,5761
Non-polymers7455
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint-10 kcal/mol
Surface area15640 Å2
MethodPISA
2
A: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,2014
Polymers41,5761
Non-polymers6253
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area15680 Å2
MethodPISA
3
C: Kinesin family member 13B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,1314
Polymers41,5761
Non-polymers5553
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint-4 kcal/mol
Surface area15250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.303, 110.303, 95.124
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: 41575.930 Da / Num. of mol.: 3 / Fragment: the motor domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Kif13b / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A0G2K8Z9
#2: 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
#3: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 550 / 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: 2.68 Å3/Da / Density % sol: 54.08 %
Crystal growTemperature: 298 K / Method: evaporation / pH: 8.1
Details: 0.2M sodium citrate dihydrate, 0.1M Bis-Tris propone, 17% w/v PEG 3350

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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→50 Å / Num. obs: 85440 / % possible obs: 97.7 % / Redundancy: 8 % / Biso Wilson estimate: 34.49 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.072 / Net I/σ(I): 23.8
Reflection shellResolution: 2→2.04 Å / Rmerge(I) obs: 0.815 / Mean I/σ(I) obs: 3.2 / Num. unique obs: 8768 / CC1/2: 0.81 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

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

3gbj


Resolution: 2→36.105 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 27.5
RfactorNum. reflection% reflection
Rfree0.24 1966 2.34 %
Rwork0.189 --
obs0.1902 83974 96.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 135.52 Å2 / Biso mean: 51.9329 Å2 / Biso min: 18.86 Å2
Refinement stepCycle: final / Resolution: 2→36.105 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7535 0 113 550 8198
Biso mean--52.37 50.8 -
Num. residues----983
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077837
X-RAY DIFFRACTIONf_angle_d0.93510617
X-RAY DIFFRACTIONf_chiral_restr0.0531218
X-RAY DIFFRACTIONf_plane_restr0.0061345
X-RAY DIFFRACTIONf_dihedral_angle_d6.7736474
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 (%)
2.0002-2.05020.31161486087100
2.0502-2.10560.2611426028100
2.1056-2.16760.29651506147100
2.1676-2.23750.3193102448674
2.2375-2.3175102453774
2.3175-2.41020.27531466053100
2.4102-2.51990.2751466141100
2.5199-2.65270.25371376124100
2.6527-2.81890.24661486076100
2.8189-3.03640.27041446128100
3.0364-3.34180.25451520.19276079100
3.3418-3.82490.21391540.1687604999
3.8249-4.81710.1971500.13786062100
4.81710.19911450.164601198
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)
18.81827.50676.61098.29996.13065.168-0.19940.12370.1525-0.12270.15230.0097-0.08690.25460.02450.3534-0.02260.01030.2458-0.01440.2348-0.704158.367114.6301
22.15230.23330.50222.1357-0.72894.0149-0.00730.3269-0.08150.0274-0.0174-0.14930.37910.201-0.00070.2992-0.020.040.2058-0.0480.2178-9.865457.21890.6277
32.8021.2919-4.2172.0832-1.42818.56920.04910.23780.49130.1170.13240.30920.0808-0.5994-0.22790.39890.0616-0.01530.44760.04370.4598-27.126468.36080.3518
42.755-0.10821.19241.27-1.32652.76580.02710.0071-0.24520.02440.18310.29570.3158-0.4466-0.19450.3401-0.09240.04410.2624-0.01440.2869-22.570953.33796.2668
51.23370.592-0.35692.3287-1.52623.7673-0.04870.08330.0552-0.15310.13520.16460.0969-0.3591-0.05750.13820.02560.00160.2373-0.01470.2372-58.819640.061732.6223
61.99920.3645-0.52463.10940.8068.6329-0.0214-0.0850.3373-0.17440.2094-0.2632-1.06750.6949-0.1390.374-0.08690.07030.3983-0.05470.453-40.539757.138527.4642
72.05610.7581-1.68561.5391-0.23523.02160.1307-0.05990.36860.02170.0736-0.0062-0.5032-0.0055-0.18080.2750.03990.02320.234-0.02320.3269-51.860954.438933.4394
89.3454-6.9054-6.41015.14944.77154.40360.14070.4270.09850.0008-0.19-0.1828-0.2154-0.25970.19430.289-0.020.01850.3047-0.01710.3134-50.864496.5259-21.1794
99.0360.64643.03224.3472.62929.22750.0417-0.10660.9755-0.1048-0.0276-0.2488-1.05320.26090.06310.4382-0.10120.0840.302-0.03450.5222-43.5454101.5241-24.6524
103.3962-0.3303-0.43192.63341.30413.88630.08610.4794-0.2886-0.1433-0.003-0.21680.26390.2652-0.06440.24880.0520.030.3126-0.03150.301-45.734481.3293-38.5371
118.0029-1.9675-0.60444.9574-0.40895.91790.1041-0.4986-1.00640.65830.39750.12630.9332-0.0965-0.46240.58450.0007-0.06960.3108-0.10880.6201-50.362869.0094-36.894
124.1408-0.25040.13673.3841.05393.96870.0117-0.1363-0.65350.30080.1298-0.14820.79640.3926-0.02280.33520.1247-0.05620.3002-0.02290.4128-40.890175.1902-31.6643
133.3386-1.12810.38025.2306-0.76831.1454-0.1765-0.4273-0.56150.46010.1677-0.6240.56790.89550.03260.41150.1898-0.04410.57020.05770.4702-36.000177.2813-24.3504
141.7487-2.4841-3.10354.6284.67927.69430.05910.5736-0.31040.5124-0.0019-0.66340.52910.2768-0.11850.18990.0984-0.04390.7212-0.21020.5627-34.219183.8245-28.664
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 4 through 27 )B4 - 27
2X-RAY DIFFRACTION2chain 'B' and (resid 28 through 154 )B28 - 154
3X-RAY DIFFRACTION3chain 'B' and (resid 155 through 207 )B155 - 207
4X-RAY DIFFRACTION4chain 'B' and (resid 208 through 369 )B208 - 369
5X-RAY DIFFRACTION5chain 'A' and (resid 4 through 137 )A4 - 137
6X-RAY DIFFRACTION6chain 'A' and (resid 138 through 193 )A138 - 193
7X-RAY DIFFRACTION7chain 'A' and (resid 194 through 370 )A194 - 370
8X-RAY DIFFRACTION8chain 'C' and (resid 4 through 27 )C4 - 27
9X-RAY DIFFRACTION9chain 'C' and (resid 28 through 75 )C28 - 75
10X-RAY DIFFRACTION10chain 'C' and (resid 76 through 160 )C76 - 160
11X-RAY DIFFRACTION11chain 'C' and (resid 161 through 207 )C161 - 207
12X-RAY DIFFRACTION12chain 'C' and (resid 208 through 293 )C208 - 293
13X-RAY DIFFRACTION13chain 'C' and (resid 294 through 333 )C294 - 333
14X-RAY DIFFRACTION14chain 'C' and (resid 334 through 369 )C334 - 369

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