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- PDB-7o0s: Crystal structure of the N-terminal domain of CEP164(1-109) bound... -

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Basic information

Entry
Database: PDB / ID: 7o0s
TitleCrystal structure of the N-terminal domain of CEP164(1-109) bound to camelid nanobody 36Z
Components
  • Centrosomal protein of 164 kDa
  • Nanobody 36Z
KeywordsSTRUCTURAL PROTEIN / Centriole Centrosome Basal body Ciliogenesis
Function / homology
Function and homology information


ciliary transition fiber / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition ...ciliary transition fiber / cilium assembly / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / centriole / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / cell division / intracellular membrane-bounded organelle / DNA repair / centrosome / extracellular space / nucleoplasm / cytosol
Similarity search - Function
: / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain
Similarity search - Domain/homology
Centrosomal protein of 164 kDa
Similarity search - Component
Biological speciesCamelidae mixed library (mammal)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
Authorse Silva, I.R. / van Breugel, M.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MC_UP_1201/3 United Kingdom
CitationJournal: Structure / Year: 2022
Title: Molecular mechanisms underlying the role of the centriolar CEP164-TTBK2 complex in ciliopathies.
Authors: Rosa E Silva, I. / Bino, L. / Johnson, C.M. / Rutherford, T.J. / Neuhaus, D. / Andreeva, A. / Cajanek, L. / van Breugel, M.
History
DepositionMar 26, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 15, 2021Provider: repository / Type: Initial release
Revision 1.1Sep 22, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / diffrn_source / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Jan 19, 2022Group: Data collection / Database references / Category: citation / diffrn_source
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.year / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 21, 2022Group: Database references / Category: citation / Item: _citation.page_last
Revision 1.4Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody 36Z
B: Centrosomal protein of 164 kDa


Theoretical massNumber of molelcules
Total (without water)26,1772
Polymers26,1772
Non-polymers00
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: The nanobody binds the CEP164 N-terminal target through its CDR3 loop, as expected.
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint-6 kcal/mol
Surface area11330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.258, 50.558, 119.867
Angle α, β, γ (deg.)90.000, 98.951, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z+1/2
#4: -x+1/2,y+1/2,-z+1/2

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Components

#1: Antibody Nanobody 36Z


Mass: 13226.526 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelidae mixed library (mammal) / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Centrosomal protein of 164 kDa / Cep164


Mass: 12950.511 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEP164, KIAA1052, NPHP15 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9UPV0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / 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: 2.33 Å3/Da / Density % sol: 47.3 %
Crystal growTemperature: 292 K / Method: vapor diffusion / Details: 0.18 M tri-ammonium citrate, 20 % (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97942 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Feb 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97942 Å / Relative weight: 1
ReflectionResolution: 1.7→59.2 Å / Num. obs: 25042 / % possible obs: 100 % / Redundancy: 6.6 % / Biso Wilson estimate: 24.9 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.061 / Net I/σ(I): 6.1
Reflection shellResolution: 1.7→1.73 Å / Redundancy: 6.5 % / Rmerge(I) obs: 1.658 / Mean I/σ(I) obs: 1 / Num. unique obs: 1331 / CC1/2: 0.798 / Rpim(I) all: 0.7 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.7.0009refinement
PHENIX1.18_3845refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7O06

7o06


Resolution: 1.7→59.2 Å / SU ML: 0.2127 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.5332
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2411 1259 5.04 %
Rwork0.2019 23698 -
obs0.2039 24957 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 31.8 Å2
Refinement stepCycle: LAST / Resolution: 1.7→59.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1719 0 0 150 1869
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00591803
X-RAY DIFFRACTIONf_angle_d0.81282458
X-RAY DIFFRACTIONf_chiral_restr0.0536261
X-RAY DIFFRACTIONf_plane_restr0.005329
X-RAY DIFFRACTIONf_dihedral_angle_d5.9333252
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.770.44331460.40372606X-RAY DIFFRACTION99.46
1.77-1.850.39341160.32992615X-RAY DIFFRACTION99.49
1.85-1.950.33651380.28582618X-RAY DIFFRACTION99.6
1.95-2.070.32121390.24272614X-RAY DIFFRACTION99.42
2.07-2.230.26451470.20832611X-RAY DIFFRACTION99.67
2.23-2.450.26721340.20922650X-RAY DIFFRACTION99.71
2.45-2.810.26241360.19912630X-RAY DIFFRACTION99.78
2.81-3.530.19281580.18592643X-RAY DIFFRACTION100
3.54-59.20.18271450.15192711X-RAY DIFFRACTION99.93
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)
16.526590029561.1765072612-0.8920292360396.37696622188-0.7916408567674.49995655569-0.1141277081720.5370561004870.107982121629-0.5184037232570.0547890019441-0.2542517083320.008622849922610.128625736084-0.006827913486550.2739634799730.04654665189920.0164562055350.413582502997-0.01416032045730.260923069129-13.819381741-3.4320434088-46.400963111
20.578092686839-0.1664851259950.7358413310040.773979873260.5949247437241.649075776930.03315417758520.148341934410.195718149898-0.05595071761480.04529004735590.00971844098931-0.4547392978730.3405749671050.1111666040440.305518925462-0.05713957376190.0261071910850.3519748248530.0002262123763140.329801464004-11.21491355654.69202230112-31.4300286075
32.42196338722-0.3185163845850.3956512798032.62568548649-0.5914206484782.78764421255-0.0403836062823-0.04212784131940.05409210374520.3240889173330.1108630492420.152932615458-0.093013924344-0.4635167942430.0004421875589540.309676565788-0.001104072107590.015195851890.311980776249-0.01161058420790.262451590522-15.4362745733-3.66772944367-12.8049249643
41.75145365042-0.07411759685540.7323749099040.81626449297-0.004268844045951.66616302730.0258285860693-0.149801403657-0.05295797081080.02967307412730.01284773017540.02444053213220.0176945725511-0.085530593421-0.03134717723520.2298579833450.0027411635280.008769726278240.2411359332280.0151054999720.239374313354-10.0383648872-9.43549481373-33.1793190364
53.47697648991-0.3325614011890.4657546859872.79094634637-1.050816563914.865343370570.107995815766-0.155322891496-0.1600908894230.1234032407350.147867328316-0.4028563686850.3485310222470.299270038791-0.05675753231270.2920574560380.0226689319255-0.01053026163120.233560112668-0.005611420639510.392005132512-6.90982796216-11.432459928-11.58773615
65.035449039560.128101685671.829765870852.555357029330.3584294659251.779845141140.106188512029-0.711549996513-0.004820400904610.5828138193020.07236699237880.0948271518634-0.161905013958-0.0330851819980.0585903276680.3199858651450.01705979959440.001348355136360.563319403159-0.01201497103570.254072591701-31.97838021314.53423718224-31.3640329827
71.71764365362-0.242173344756-0.8606271325771.50735406457-0.3796588264216.27463646854-0.1856980991630.3452790788380.03743624903160.02637185890950.2258922883370.100219726092-0.0807754205429-0.44260144414-0.03697365782720.2786234981360.0181377228744-0.008060853435540.4839986131880.02671645202080.252526104133-43.29254729080.504107013447-50.8962470311
81.47072076507-0.3713712327420.4366858447120.668352233354-0.03670570938081.38441358669-0.00666405177951-0.1585330813030.0545141038690.05702256237170.0483991217599-0.123389330896-0.0621480563282-0.1536041900110.05984039758470.2224325522440.003154471513190.003354107822640.2554175947070.0007675803540660.238218995211-27.04333062464.02357924212-37.6132784706
91.948046034330.8946850618950.09429452493882.43650678124-0.5505017726961.10846991327-0.04632569020630.00304078479936-0.0728565510806-0.1659336797920.081659406206-0.03752143598630.1379000119560.074855333133-0.04667303140670.241537371154-0.01156622765920.01412340101350.2149698367860.01189085576880.280316245394-27.0987822577-7.21653936616-43.1413640191
102.33364703276-0.01970170394511.272264924021.076423088190.1210998416742.63865789762-0.1003270944370.4566018611310.0470497239507-0.3219563398310.0690723438256-0.234757739768-0.1279380097870.09636328260530.008757414516290.2750724811160.0254303784610.03350179494020.3067757015610.01949321838070.233783611291-22.6848821141.1243277334-50.6996488895
112.574002124770.2927522345491.787617030841.999585734281.456722331294.68291406304-0.07635168317280.3746888837640.298677973054-0.228551449681-0.08074975334360.0846367138493-0.5454103930320.05111806226320.1385479359820.2899066668380.0126676041146-0.003297878721710.2602660699920.01010778324850.244564540222-26.93964790158.31692042193-43.0140057654
122.563794929970.849148502931-0.06555510913574.15844647077-3.060527080974.199724515250.007920927426250.368069117267-0.0585849892795-0.731799623048-0.0787286894612-0.0305141661070.393131397881-0.0946576318905-0.03324201318720.334741402676-0.03458098185580.01899503684130.369291278746-0.02904648259770.266329138145-36.9318868654-3.93808412417-52.8648449306
131.32825352593-0.2931233580181.004088896980.396578968924-0.09132560432231.51682452562-0.0700583269861-0.147590282120.1777617214080.00738294604645-0.0272039918083-0.0164561065884-0.009356830753410.09537124480440.0001023107216290.2661793385950.00210416988066-0.005029216536140.1951775010630.0005295277569320.261216039007-23.2087408833-1.55124019207-33.1312899497
144.51437776927-0.2098071309992.907856061921.52352163284-0.6575134189284.32663582266-0.112013176487-0.3430724906070.14952660458-0.0870125821132-0.1154169836830.06749989416720.228781297511-0.571697962496-0.03203404757860.274107185116-0.0313722211976-0.004729389624310.3102839300360.01044845856350.207769004531-40.3292084042-3.38155631615-43.2286734916
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'B' and (resid 2 through 11 )BB2 - 111 - 10
22chain 'B' and (resid 12 through 25 )BB12 - 2511 - 24
33chain 'B' and (resid 26 through 55 )BB26 - 5525 - 56
44chain 'B' and (resid 56 through 88 )BB56 - 8857 - 89
55chain 'B' and (resid 89 through 105 )BB89 - 10490 - 107
66chain 'A' and (resid 3 through 11 )AA3 - 111 - 9
77chain 'A' and (resid 12 through 19 )AA12 - 1910 - 17
88chain 'A' and (resid 20 through 40 )AA20 - 4018 - 40
99chain 'A' and (resid 41 through 53 )AA41 - 5341 - 53
1010chain 'A' and (resid 54 through 67 )AA54 - 6754 - 71
1111chain 'A' and (resid 68 through 83 )AA68 - 8372 - 87
1212chain 'A' and (resid 84 through 91 )AA84 - 9188 - 95
1313chain 'A' and (resid 92 through 109 )AA92 - 10996 - 113
1414chain 'A' and (resid 110 through 119 )AA110 - 119114 - 125

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