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- PDB-5ybv: The structure of the KANK2 ankyrin domain with the KIF21A peptide -

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Basic information

Entry
Database: PDB / ID: 5ybv
TitleThe structure of the KANK2 ankyrin domain with the KIF21A peptide
Components
  • (KN motif and ankyrin repeat domain-containing protein ...) x 2
  • Kinesin-like protein KIF21A
KeywordsCELL ADHESION
Function / homology
Function and homology information


negative regulation of vitamin D receptor signaling pathway / kidney epithelium development / regulation of microtubule depolymerization / regulation of axon guidance / podocyte cell migration / negative regulation of actin filament polymerization / negative regulation of intracellular estrogen receptor signaling pathway / cortical microtubule organization / regulation of Rho protein signal transduction / ankyrin repeat binding ...negative regulation of vitamin D receptor signaling pathway / kidney epithelium development / regulation of microtubule depolymerization / regulation of axon guidance / podocyte cell migration / negative regulation of actin filament polymerization / negative regulation of intracellular estrogen receptor signaling pathway / cortical microtubule organization / regulation of Rho protein signal transduction / ankyrin repeat binding / anterograde axonal transport / plus-end-directed microtubule motor activity / Kinesins / kinesin complex / microtubule motor activity / negative regulation of programmed cell death / COPI-dependent Golgi-to-ER retrograde traffic / microtubule-based movement / negative regulation of G1/S transition of mitotic cell cycle / regulation of microtubule polymerization / axonal growth cone / axon cytoplasm / presynapse / cell cortex / microtubule binding / microtubule / negative regulation of cell population proliferation / apoptotic process / dendrite / negative regulation of transcription by RNA polymerase II / ATP hydrolysis activity / mitochondrion / ATP binding / cytoplasm / cytosol
Similarity search - Function
: / : / KIF21A-like domain / KIF21A-like domain / Kank N-terminal motif / KN motif / : / Kinesin-like protein / Ankyrin repeat-containing domain / Kinesin motor domain signature. ...: / : / KIF21A-like domain / KIF21A-like domain / Kank N-terminal motif / KN motif / : / Kinesin-like protein / Ankyrin repeat-containing 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 / Kinesin motor domain superfamily / Ankyrin repeat / Ankyrin repeats (3 copies) / Ankyrin repeat profile. / Ankyrin repeat region circular profile. / ankyrin repeats / Ankyrin repeat / Ankyrin repeat-containing domain superfamily / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / WD domain, G-beta repeat / WD40 repeat, conserved site / Trp-Asp (WD) repeats signature. / Trp-Asp (WD) repeats profile. / Trp-Asp (WD) repeats circular profile. / WD40 repeats / WD40 repeat / WD40-repeat-containing domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / P-loop containing nucleoside triphosphate hydrolase / Mainly Alpha
Similarity search - Domain/homology
KN motif and ankyrin repeat domain-containing protein 2 / Kinesin-like protein KIF21A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsGuo, Q. / Liao, S. / Min, J. / Xu, C. / Structural Genomics Consortium (SGC)
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis for the recognition of kinesin family member 21A (KIF21A) by the ankyrin domains of KANK1 and KANK2 proteins.
Authors: Guo, Q. / Liao, S. / Zhu, Z. / Li, Y. / Li, F. / Xu, C.
History
DepositionSep 5, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 6, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 22, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: KN motif and ankyrin repeat domain-containing protein 2
B: KN motif and ankyrin repeat domain-containing protein 2
C: Kinesin-like protein KIF21A
D: Kinesin-like protein KIF21A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,31110
Polymers61,7514
Non-polymers5616
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5450 Å2
ΔGint-46 kcal/mol
Surface area22690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.956, 52.834, 53.478
Angle α, β, γ (deg.)73.02, 89.67, 84.91
Int Tables number1
Space group name H-MP1

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Components

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KN motif and ankyrin repeat domain-containing protein ... , 2 types, 2 molecules AB

#1: Protein KN motif and ankyrin repeat domain-containing protein 2 / Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1- ...Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1-interacting protein / SRC1-interacting protein


Mass: 28057.035 Da / Num. of mol.: 1 / Fragment: UNP residues 578-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KANK2, ANKRD25, KIAA1518, MXRA3, SIP
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: Q63ZY3
#2: Protein KN motif and ankyrin repeat domain-containing protein 2 / Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1- ...Ankyrin repeat domain-containing protein 25 / Matrix-remodeling-associated protein 3 / SRC-1-interacting protein / SRC1-interacting protein


Mass: 28383.428 Da / Num. of mol.: 1 / Fragment: UNP residues 578-832
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KANK2, ANKRD25, KIAA1518, MXRA3, SIP
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: Q63ZY3

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Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide Kinesin-like protein KIF21A / Kinesin-like protein KIF2 / Renal carcinoma antigen NY-REN-62


Mass: 2655.081 Da / Num. of mol.: 2 / Fragment: UNP residues 1146-1167 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q7Z4S6

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Non-polymers , 3 types, 185 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 179 / 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 Å3/Da / Density % sol: 38.58 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES (pH7.5), 0.15M ammonium acetate, 31 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9796 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 8, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2.12→34.47 Å / Num. obs: 25270 / % possible obs: 92.9 % / Redundancy: 3.8 % / Net I/σ(I): 10.2

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Processing

Software
NameVersionClassification
PHENIXdev_2722refinement
HKL-2000data processing
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4HBD

4hbd


Resolution: 2.12→34.467 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 28.05
RfactorNum. reflection% reflection
Rfree0.235 2002 7.92 %
Rwork0.1883 --
obs0.192 25270 92.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.12→34.467 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3880 0 34 179 4093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013984
X-RAY DIFFRACTIONf_angle_d1.2775406
X-RAY DIFFRACTIONf_dihedral_angle_d20.771448
X-RAY DIFFRACTIONf_chiral_restr0.067661
X-RAY DIFFRACTIONf_plane_restr0.005692
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.12-2.17310.39711430.33121666X-RAY DIFFRACTION93
2.1731-2.23180.38811430.31541676X-RAY DIFFRACTION93
2.2318-2.29750.31711470.27651696X-RAY DIFFRACTION93
2.2975-2.37160.33061390.25871661X-RAY DIFFRACTION94
2.3716-2.45630.29751450.25051644X-RAY DIFFRACTION93
2.4563-2.55470.27451430.23611702X-RAY DIFFRACTION94
2.5547-2.67090.28921360.21941685X-RAY DIFFRACTION94
2.6709-2.81160.30211500.22491690X-RAY DIFFRACTION94
2.8116-2.98770.27011440.21891646X-RAY DIFFRACTION93
2.9877-3.21820.23581470.18691673X-RAY DIFFRACTION93
3.2182-3.54180.24321410.18361639X-RAY DIFFRACTION91
3.5418-4.05360.18711410.14561585X-RAY DIFFRACTION90
4.0536-5.10450.16081410.13341669X-RAY DIFFRACTION93
5.1045-34.47120.17061420.14231636X-RAY DIFFRACTION92
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)
10.8448-0.5255-0.43451.077-0.34590.7082-0.0070.49140.2290.0836-0.0975-0.10550.46750.4028-00.38060.0336-0.00440.3309-0.01650.473512.7793-22.81510.9117
21.4367-1.5816-0.20112.4969-0.52251.52110.21470.0418-0.12950.6079-0.0241-0.45740.03670.20410.00860.3159-0.0057-0.00060.3766-0.02220.33910.2085-17.65572.966
30.1613-0.08440.18580.1291-0.09540.2012-0.1470.2555-0.3162-0.0388-0.33750.45570.1117-0.1694-00.36310.0308-0.02060.3257-0.01520.34336.1975-17.1209-5.4444
40.6524-0.31410.53491.32320.0280.51630.1129-0.03010.24810.3327-0.0053-0.1254-0.02460.070600.2095-0.01190.02010.3484-0.01680.27855.379-5.04471.8611
51.0309-1.19550.72621.7511-0.33571.33470.04710.0529-0.0056-0.0255-0.1384-0.0637-0.1110.1068-00.1679-0.03030.04690.3192-0.00910.24581.42332.4211-1.6267
61.3122-0.68750.43251.54140.02190.3031-0.0777-0.18190.15490.058-0.0784-0.06180.00960.057300.1843-0.02150.05360.3016-0.01960.3072-6.29778.4952-1.3684
71.6338-0.57210.60991.00470.0110.5472-0.1382-0.25910.3221-0.0586-0.12430.2675-0.2004-0.3107-0.00480.2059-0.01140.01410.3799-0.06670.3134-12.205415.8182-1.3219
80.0148-0.00490.01950.1248-0.02810.029-0.1147-0.3033-0.35180.0731-0.00350.89-0.1684-0.12230.00080.47320.05930.0870.6637-0.10170.4356-18.483811.19647.5537
90.0110.013-0.01110.0153-0.00660.04150.41530.24630.041-0.0226-0.2483-0.3225-0.10260.525700.52660.07050.1230.6565-0.02590.4689-7.37515.164411.6685
100.8751-0.85270.20081.1576-0.30360.0831-0.2112-1.48760.65041.24420.4074-0.3663-0.0172-0.0150.0020.73420.0078-0.02180.5992-0.05910.3514-5.5627-2.882211.3813
110.0135-0.009-0.00560.01260.01130.0193-0.21820.2748-0.323-0.22280.26990.22260.1874-0.1178-00.4408-0.01060.04820.3319-0.10520.499516.2806-53.0985-24.1832
120.0333-0.0507-0.01780.06660.02710.04710.12820.5069-0.1498-0.138-0.1717-0.0284-0.17060.2512-0.00010.72960.0603-0.14290.6791-0.16720.58849.8334-44.0252-30.2974
130.13650.0750.01890.04240.00740.0049-0.13530.8454-0.6143-0.7003-0.18360.85140.082-0.0174-00.6348-0.0082-0.1340.5435-0.0680.51463.4482-39.2519-28.2728
140.6745-0.00760.10990.73290.20150.10810.54330.07010.03240.12220.2806-0.08790.35520.5286-00.60890.1606-0.04420.5255-0.04510.6193-6.8015-12.2588-22.4921
151.736-0.06870.55130.8957-0.43620.5820.1520.06010.1811-0.423-0.05460.3128-0.6241-0.4654-0.02910.87420.0757-0.19680.40260.07670.6628-3.5337-17.5019-24.1268
165.09430.25810.11030.03820.05560.0969-0.0447-0.70420.60380.1061-0.31321.7419-0.1011-0.2165-0.10640.61660.1006-0.10310.2509-0.07590.65420.8654-17.4426-15.8461
172.29272.26380.23952.804-0.34441.0341-0.07740.14450.5361-0.71190.12070.3372-0.4477-0.1506-0.46440.6328-0.0104-0.1770.21740.0810.28487.0752-25.0849-25.8827
181.7375-1.74180.75372.38430.20431.8512-0.24330.16670.098-0.54530.03920.0034-0.42910.3025-0.01960.5147-0.0835-0.04210.23820.04670.213314.859-29.4143-24.4568
190.5882-0.421-0.27510.4856-0.10920.63620.02820.0127-0.0822-0.2717-0.05360.0556-0.01270.2317-00.4371-0.0635-0.03320.27230.03760.285621.4984-37.7099-25.8807
200.477-0.51780.10251.3364-0.08480.6106-0.11780.022-0.3194-0.31470.0062-0.15120.33120.0449-00.354-0.01460.02960.3309-0.00810.260125.2294-45.5878-22.831
210.5136-0.55070.32740.7752-0.02540.71070.0190.1937-0.5211-0.2091-0.0146-0.10490.30970.5005-00.50260.06560.08650.4068-0.03660.396230.3683-54.0851-23.321
220.6803-0.88880.11381.1239-0.18480.5536-0.1308-0.0570.3340.0315-0.03830.2147-0.2555-0.141200.25290.0343-0.01560.4375-0.09180.4287-18.678123.4654-0.6067
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 588 through 606 )
2X-RAY DIFFRACTION2chain 'A' and (resid 607 through 651 )
3X-RAY DIFFRACTION3chain 'A' and (resid 652 through 661 )
4X-RAY DIFFRACTION4chain 'A' and (resid 662 through 691 )
5X-RAY DIFFRACTION5chain 'A' and (resid 692 through 729 )
6X-RAY DIFFRACTION6chain 'A' and (resid 730 through 762 )
7X-RAY DIFFRACTION7chain 'A' and (resid 763 through 796 )
8X-RAY DIFFRACTION8chain 'C' and (resid 1152 through 1155 )
9X-RAY DIFFRACTION9chain 'C' and (resid 1156 through 1160)
10X-RAY DIFFRACTION10chain 'C' and (resid 1161 through 1166 )
11X-RAY DIFFRACTION11chain 'D' and (resid 1152 through 1155 )
12X-RAY DIFFRACTION12chain 'D' and (resid 1156 through 1160 )
13X-RAY DIFFRACTION13chain 'D' and (resid 1161 through 1166 )
14X-RAY DIFFRACTION14chain 'B' and (resid 588 through 606 )
15X-RAY DIFFRACTION15chain 'B' and (resid 607 through 651 )
16X-RAY DIFFRACTION16chain 'B' and (resid 652 through 661 )
17X-RAY DIFFRACTION17chain 'B' and (resid 662 through 691 )
18X-RAY DIFFRACTION18chain 'B' and (resid 692 through 729 )
19X-RAY DIFFRACTION19chain 'B' and (resid 739 through 762 )
20X-RAY DIFFRACTION20chain 'B' and (resid 763 through 796 )
21X-RAY DIFFRACTION21chain 'B' and (resid 797 through 830 )
22X-RAY DIFFRACTION22chain 'A' and (resid 797 through 831 )

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