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- PDB-4ejq: Crystal structure of KIF1A C-CC1-FHA -

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Basic information

Entry
Database: PDB / ID: 4ejq
TitleCrystal structure of KIF1A C-CC1-FHA
ComponentsKinesin-like protein KIF1A
KeywordsTRANSPORT PROTEIN / HOMODIMER / FHA DOMAIN
Function / homology
Function and homology information


neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Kinesins / plus-end-directed microtubule motor activity ...neuronal dense core vesicle membrane / dense core granule cytoskeletal transport / anterograde neuronal dense core vesicle transport / retrograde neuronal dense core vesicle transport / regulation of dendritic spine development / cytoskeleton-dependent intracellular transport / regulation of dendritic spine morphogenesis / anterograde axonal transport / Kinesins / plus-end-directed microtubule motor activity / COPI-dependent Golgi-to-ER retrograde traffic / kinesin complex / microtubule-based movement / neuronal dense core vesicle / cytoskeletal motor activity / vesicle-mediated transport / axon cytoplasm / microtubule binding / microtubule / axon / synapse / dendrite / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / identical protein binding
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2530 / : / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Tumour Suppressor Smad4 - #20 / Kinesin-associated / Kinesin-associated ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2530 / : / : / Kinesin-like KIF1-type / Kinesin protein 1B / Kinesin-like / Kinesin protein / Tumour Suppressor Smad4 - #20 / Kinesin-associated / Kinesin-associated / Tumour Suppressor Smad4 / Forkhead associated domain / Forkhead-associated (FHA) domain profile. / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Kinesin motor domain superfamily / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / Helix non-globular / Special / PH-like domain superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Kinesin-like protein KIF1A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.893 Å
AuthorsHuo, L. / Yue, Y. / Ren, J. / Yu, J. / Liu, J. / Yu, Y. / Ye, F. / Xu, T. / Zhang, M. / Feng, W.
CitationJournal: Structure / Year: 2012
Title: The CC1-FHA Tandem as a Central Hub for Controlling the Dimerization and Activation of Kinesin-3 KIF1A
Authors: Huo, L. / Yue, Y. / Ren, J. / Yu, J. / Liu, J. / Yu, Y. / Ye, F. / Xu, T. / Zhang, M. / Feng, W.
History
DepositionApr 6, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 3, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Kinesin-like protein KIF1A
B: Kinesin-like protein KIF1A
C: Kinesin-like protein KIF1A
D: Kinesin-like protein KIF1A
E: Kinesin-like protein KIF1A
F: Kinesin-like protein KIF1A
G: Kinesin-like protein KIF1A
H: Kinesin-like protein KIF1A


Theoretical massNumber of molelcules
Total (without water)139,0298
Polymers139,0298
Non-polymers00
Water11,854658
1
A: Kinesin-like protein KIF1A
B: Kinesin-like protein KIF1A


Theoretical massNumber of molelcules
Total (without water)34,7572
Polymers34,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4030 Å2
ΔGint-28 kcal/mol
Surface area15520 Å2
MethodPISA
2
C: Kinesin-like protein KIF1A
D: Kinesin-like protein KIF1A


Theoretical massNumber of molelcules
Total (without water)34,7572
Polymers34,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-26 kcal/mol
Surface area15630 Å2
MethodPISA
3
E: Kinesin-like protein KIF1A
F: Kinesin-like protein KIF1A


Theoretical massNumber of molelcules
Total (without water)34,7572
Polymers34,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-26 kcal/mol
Surface area15880 Å2
MethodPISA
4
G: Kinesin-like protein KIF1A
H: Kinesin-like protein KIF1A


Theoretical massNumber of molelcules
Total (without water)34,7572
Polymers34,7572
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-28 kcal/mol
Surface area15870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.945, 57.844, 110.394
Angle α, β, γ (deg.)89.980, 89.960, 90.630
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Kinesin-like protein KIF1A / Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A- ...Axonal transporter of synaptic vesicles / Microtubule-based motor KIF1A / Unc-104- and KIF1A-related protein / hUnc-104


Mass: 17378.625 Da / Num. of mol.: 8 / Fragment: C-CC1-FHA, UNP residues 458-607
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KIF1A, ATSV, C2orf20 / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q12756
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / 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: 1.97 Å3/Da / Density % sol: 37.64 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2 M calcium acetate hydrate, 18% (w/v) PEG 3000, 0.1 M Bis-Tris, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 3, 2011 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.893→50 Å / Num. obs: 82040 / Redundancy: 3.9 %
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4 % / % possible all: 96.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
MAR345dtbdata collection
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.7_650refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4EGX
Resolution: 1.893→33.906 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.21 / σ(F): 0.1 / Phase error: 24.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 1961 2.46 %RANDOM
Rwork0.1872 ---
obs0.1883 79571 94 %-
Solvent computationShrinkage radii: 0.61 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.323 Å2 / ksol: 0.366 e/Å3
Displacement parametersBiso max: 263.63 Å2 / Biso mean: 44.1785 Å2 / Biso min: 11.06 Å2
Baniso -1Baniso -2Baniso -3
1-6.0632 Å22.8295 Å21.1413 Å2
2---5.3905 Å2-0.4277 Å2
3----0.6727 Å2
Refinement stepCycle: LAST / Resolution: 1.893→33.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9396 0 0 658 10054
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.007
X-RAY DIFFRACTIONf_angle_d1.109
X-RAY DIFFRACTIONf_dihedral_angle_d16.775
X-RAY DIFFRACTIONf_chiral_restr0.075
X-RAY DIFFRACTIONf_plane_restr0.004
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.0002-0.00020.00080.00390.00250.0122-0.0251-0.01-0.03650.0253-0.0012-0.0297-0.00040.01720.00150.405-0.1218-0.26260.1024-0.07020.08361.7433-5.16485.67
20.083-0.0624-0.04580.04990.03760.0208-0.0113-0.05510.04660.05630.0536-0.0711-0.0213-0.0121-0.01730.07930.0325-0.00350.0984-0.00540.1053-12.7898-11.141669.4348
30.15480.0507-0.05010.04630.02720.10440.0206-0.02420.05370.04610.00650.02710.0319-0.0031-0.00830.0021-0.00010.13040.12970.02640.0244-25.1043-18.061670.5983
40.0580.0023-0.0420.0132-0.00850.0506-0.01050.0165-0.0104-0.0134-0.00780.00040.04820.03150.00560.11980.01910.02350.11080.00750.0943-9.4732-27.326365.5188
50.0131-0.0159-0.0040.03320.00550.005-0.02860.02420.01990.00630.1113-0.06740.0366-0.0498-0.0157-0.4252-0.15760.26410.08270.0922-0.0635-17.9353-17.848259.0949
60.09840.0015-0.00540.0079-0.00540.00360.00620.02320.0166-0.01490.01680.01120.01150.0503-0.01160.03570.0817-0.13150.19-0.06670.19073.4013-20.298759.8482
70.0229-0.0268-0.01460.03140.01820.0105-0.0524-0.03910.0212-0.02150.02050.0125-0.00140.01890.01180.55920.2703-0.19280.3148-0.02110.3032-8.2425-7.653492.1337
80.0485-0.04010.05460.0347-0.04180.08510.0080.0015-0.00360.0192-0.00250.0049-0.05950.0229-0.00420.4024-0.0101-0.01140.32090.13740.1849-13.7665-12.000380.1298
90.59350.2787-0.05340.3191-0.23030.2411-0.0456-0.0546-0.12920.2093-0.0464-0.0903-0.1606-0.0110.0160.10180.12230.0472-0.0811-0.140.0246-3.71381.534169.1728
100.03560.0072-0.02130.0019-0.00420.0123-0.02460.0118-0.0331-0.1026-0.003-0.08460.00350.00270.01370.33530.04470.01890.1988-0.03880.24046.37133.732267.4434
110.4107-0.146-0.31840.07190.14440.34440.1743-0.01570.3583-0.1122-0.0018-0.04-0.38230.0052-0.13520.28020.02540.04120.1662-0.01930.2692-4.262211.932563.9885
120.03180.009-0.03080.06510.05320.09330.025-0.02920.03060.0315-0.04620.01140.0054-0.004-0.00240.19820.1233-0.18940.11740.01230.0638-23.6615-18.057715.7033
130.1042-0.0478-0.11090.48460.19810.1580.0550.0268-0.0109-0.2102-0.0864-0.0313-0.081-0.05750.00380.1524-0.0228-0.01780.13210.00160.1131-13.9953-14.302934.8249
140.6534-0.1994-0.24270.25710.0050.2591-0.198-0.07970.1272-0.04650.2247-0.05460.12790.03440.00630.13880.00240.03280.1255-0.03420.1281-2.9315-28.728140.7882
150.0373-0.05080.03260.0733-0.04520.0294-0.0533-0.0050.04470.08980.0346-0.0295-0.0324-0.00830.02160.2379-0.0516-0.08650.20280.01170.222-13.4787-16.884614.3052
160.3626-0.4014-0.02290.73890.12150.02560.0390.0547-0.0716-0.2663-0.02710.0647-0.0488-0.0695-0.02880.1518-0.0181-0.00050.12880.01570.0962-18.6577-9.882836.2327
170.1209-0.12890.12780.1930.01820.3896-0.0334-0.05940.086-0.15310.0659-0.1662-0.266-0.1085-0.02580.1789-0.01260.03430.07510.02160.1252-16.48082.02543.613
180.2165-0.0386-0.11270.085-0.07340.1777-0.1111-0.0044-0.00340.09140.0429-0.02780.0955-0.01390.05650.2739-0.01810.03430.18760.00290.1928-32.080724.630772.6801
190.3841-0.17120.05250.4237-0.13750.2841-0.0020.01170.0607-0.2358-0.04460.00990.06050.1650.00740.1323-0.0171-0.00920.1145-0.00370.0829-24.715814.844192.8145
200.02090.03460.00850.05570.01370.0035-0.00250.0080.0065-0.0062-0.0195-0.00110.00830.01080.01380.2081-0.00120.00260.2062-0.02480.1506-12.31738.303395.1194
210.2145-0.1508-0.09970.1795-0.12630.4325-0.0542-0.0507-0.047-0.10890.10870.1660.23780.0744-0.02110.1508-0.0076-0.03050.0815-0.01970.1316-26.41483.658198.8169
220.1452-0.04360.07030.2688-0.14830.1166-0.0158-0.0594-0.02080.0597-0.0462-0.026-0.0135-0.01850.00120.21670.11140.15160.12450.00880.0222-19.382323.705870.8152
230.3343-0.21960.03310.3816-0.13090.09310.02120.0442-0.093-0.2304-0.04180.08890.0370.0203-0.00860.1389-0.0403-0.00860.11050.00970.1139-32.914324.095689.4478
240.0308-0.0157-0.01140.00880.00820.00580.0122-0.0118-0.0443-0.00060.06690.08170.0112-0.0442-0.03090.2002-0.0528-0.11940.25850.06960.2635-50.166931.34390.3023
250.3983-0.22690.24860.2333-0.09160.1833-0.1737-0.1756-0.01080.14090.20750.0053-0.1372-0.08250.01220.14370.0351-0.02790.14560.01080.1108-36.621135.708899.6287
260.10980.12710.0740.16430.0920.0653-0.07540.055-0.0699-0.04590.10150.0028-0.0461-0.0041-0.04390.60050.22070.22490.29020.00460.369-34.432312.926435.3487
270.0173-0.0348-0.04680.13710.18720.2569-0.00220.00190.00260.004-0.0157-0.00310.1042-0.0140.02160.55780.0674-0.03420.4332-0.11710.4059-27.251619.17226.6264
280.0022-0.0040.01630.0063-0.02690.11510.05230.0083-0.00730.03120.01090.0020.00840.0194-0.01880.35940.0974-0.05460.2165-0.02110.1884-29.75997.541620.4199
290.53780.1398-0.19080.32660.01590.2478-0.0513-0.06240.06460.0801-0.01110.08530.07260.05170.01430.13620.02840.02360.11530.0240.1231-42.95864.258412.5877
300.0195-0.02410.0240.17740.10440.1566-0.0463-0.0015-0.0013-0.0008-0.03690.0380.01190.00230.04750.2587-0.0010.00210.23030.00610.2387-52.6458-0.516213.9056
310.11270.0793-0.12520.0565-0.08850.1399-0.0240.0029-0.0524-0.0743-0.0313-0.07270.0127-0.01080.05140.4879-0.0262-0.04020.24060.02570.3271-52.8824-1.51754.971
320.19630.05540.11590.01590.03260.13460.0122-0.019-0.0137-0.03270.01890.03440.065-0.0121-0.01750.29270.0158-0.01040.24450.13150.3841-36.0641-11.283218.6589
330.4763-0.12590.36990.0562-0.14040.41530.15630.0221-0.3051-0.15170.00660.02890.26380.015-0.11740.23750.0299-0.0330.1278-0.01990.2053-39.637-5.95715.2597
340.06170.0033-0.01080.05880.04260.03420.0261-0.0054-0.04680.0164-0.028-0.01420.0064-0.0009-0.01380.3374-0.0039-0.07490.2427-0.01520.3193-24.8936-5.283116.1622
350.00070.00010.00030.00240.00020.0006-0.06060.0069-0.0219-0.08730.008-0.02450.0334-0.01620.01050.4242-0.05810.14730.1694-0.02840.2449-45.297514.448535.5894
360.2923-0.03940.05460.12560.1360.17170.0550.05940.06520.1401-0.0118-0.02010.0924-0.0158-0.00970.1207-0.00110.01930.08250.01820.0926-35.589510.248216.3673
370.38230.13670.28240.2548-0.04790.2962-0.13830.0026-0.13380.06550.0075-0.1504-0.01020.05310.0176-0.08970.0329-0.12550.0934-0.01250.016-21.000823.788215.8059
380.0029-0.00320.02790.0511-0.0760.0883-0.02710.17230.04240.16460.12140.0874-0.1416-0.0486-0.0205-0.2594-0.017-0.15890.14970.01610.0434-30.986925.85435.2378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 454:485)A454 - 485
2X-RAY DIFFRACTION2chain 'A' and (resseq 486:519)A486 - 519
3X-RAY DIFFRACTION3chain 'A' and (resseq 520:546)A520 - 546
4X-RAY DIFFRACTION4chain 'A' and (resseq 547:559)A547 - 559
5X-RAY DIFFRACTION5chain 'A' and (resseq 560:596)A560 - 596
6X-RAY DIFFRACTION6chain 'A' and (resseq 597:607)A597 - 607
7X-RAY DIFFRACTION7chain 'B' and (resseq 456:471)B456 - 471
8X-RAY DIFFRACTION8chain 'B' and (resseq 472:485)B472 - 485
9X-RAY DIFFRACTION9chain 'B' and (resseq 486:520)B486 - 520
10X-RAY DIFFRACTION10chain 'B' and (resseq 527:533)B527 - 533
11X-RAY DIFFRACTION11chain 'B' and (resseq 534:603)B534 - 603
12X-RAY DIFFRACTION12chain 'C' and (resseq 454:471)C454 - 471
13X-RAY DIFFRACTION13chain 'C' and (resseq 472:507)C472 - 507
14X-RAY DIFFRACTION14chain 'C' and (resseq 508:604)C508 - 604
15X-RAY DIFFRACTION15chain 'D' and (resseq 456:472)D456 - 472
16X-RAY DIFFRACTION16chain 'D' and (resseq 473:533)D473 - 533
17X-RAY DIFFRACTION17chain 'D' and (resseq 534:603)D534 - 603
18X-RAY DIFFRACTION18chain 'E' and (resseq 456:481)E456 - 481
19X-RAY DIFFRACTION19chain 'E' and (resseq 482:523)E482 - 523
20X-RAY DIFFRACTION20chain 'E' and (resseq 524:533)E524 - 533
21X-RAY DIFFRACTION21chain 'E' and (resseq 534:603)E534 - 603
22X-RAY DIFFRACTION22chain 'F' and (resseq 454:471)F454 - 471
23X-RAY DIFFRACTION23chain 'F' and (resseq 472:523)F472 - 523
24X-RAY DIFFRACTION24chain 'F' and (resseq 524:540)F524 - 540
25X-RAY DIFFRACTION25chain 'F' and (resseq 541:604)F541 - 604
26X-RAY DIFFRACTION26chain 'G' and (resseq 457:472)G457 - 472
27X-RAY DIFFRACTION27chain 'G' and (resseq 473:481)G473 - 481
28X-RAY DIFFRACTION28chain 'G' and (resseq 482:492)G482 - 492
29X-RAY DIFFRACTION29chain 'G' and (resseq 493:523)G493 - 523
30X-RAY DIFFRACTION30chain 'G' and (resseq 524:533)G524 - 533
31X-RAY DIFFRACTION31chain 'G' and (resseq 534:540)G534 - 540
32X-RAY DIFFRACTION32chain 'G' and (resseq 541:553)G541 - 553
33X-RAY DIFFRACTION33chain 'G' and (resseq 554:595)G554 - 595
34X-RAY DIFFRACTION34chain 'G' and (resseq 596:602)G596 - 602
35X-RAY DIFFRACTION35chain 'H' and (resseq 454:471)H454 - 471
36X-RAY DIFFRACTION36chain 'H' and (resseq 472:507)H472 - 507
37X-RAY DIFFRACTION37chain 'H' and (resseq 508:546)H508 - 546
38X-RAY DIFFRACTION38chain 'H' and (resseq 547:607)H547 - 607

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