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- PDB-3rdv: Structure of the SLAIN2c-CLIPCG1 complex -

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Basic information

Entry
Database: PDB / ID: 3rdv
TitleStructure of the SLAIN2c-CLIPCG1 complex
Components
  • CAP-Gly domain-containing linker protein 1
  • SLAIN motif-containing protein 2
KeywordsSTRUCTURAL PROTEIN / Cytoskeletal protein / CAP GLY protein complex
Function / homology
Function and homology information


microtubule nucleation / microtubule plus-end binding / microtubule bundle formation / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization ...microtubule nucleation / microtubule plus-end binding / microtubule bundle formation / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / ruffle / Resolution of Sister Chromatid Cohesion / tubulin binding / RHO GTPases Activate Formins / cytoplasmic vesicle membrane / kinetochore / Separation of Sister Chromatids / microtubule cytoskeleton / mitotic cell cycle / cell cortex / microtubule binding / microtubule / centrosome / zinc ion binding / identical protein binding / nucleus / cytosol
Similarity search - Function
SLAIN motif-containing protein / SLAIN motif-containing family / CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. ...SLAIN motif-containing protein / SLAIN motif-containing family / CLIP1, zinc knuckle / CLIP1 zinc knuckle / CAP Gly-rich-like domain / CAP-Gly domain signature. / CAP Gly-rich domain / CAP Gly-rich domain superfamily / CAP-Gly domain / CAP-Gly domain profile. / CAP_GLY / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / CAP-Gly domain-containing linker protein 1 / SLAIN motif-containing protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsManatschal, C. / Olieric, V. / Steinmetz, M.O.
CitationJournal: J.Cell Biol. / Year: 2011
Title: SLAIN2 links microtubule plus end-tracking proteins and controls microtubule growth in interphase
Authors: van der Vaart, B. / Manatschal, C. / Grigoriev, I. / Olieric, V. / Gouveia, S.M. / Bjelic, S. / Demmers, J. / Vorobjev, I. / Hoogenraad, C.C. / Steinmetz, M.O. / Akhmanova, A.
History
DepositionApr 1, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Nov 1, 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 / struct_site
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_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CAP-Gly domain-containing linker protein 1
B: CAP-Gly domain-containing linker protein 1
C: CAP-Gly domain-containing linker protein 1
D: CAP-Gly domain-containing linker protein 1
E: SLAIN motif-containing protein 2
F: SLAIN motif-containing protein 2
G: SLAIN motif-containing protein 2
H: SLAIN motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,19810
Polymers36,0978
Non-polymers1012
Water5,188288
1
A: CAP-Gly domain-containing linker protein 1
E: SLAIN motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,0473
Polymers9,0242
Non-polymers231
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-4 kcal/mol
Surface area4300 Å2
MethodPISA
2
B: CAP-Gly domain-containing linker protein 1
F: SLAIN motif-containing protein 2


Theoretical massNumber of molelcules
Total (without water)9,0242
Polymers9,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area4370 Å2
MethodPISA
3
C: CAP-Gly domain-containing linker protein 1
G: SLAIN motif-containing protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,1023
Polymers9,0242
Non-polymers781
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area850 Å2
ΔGint-5 kcal/mol
Surface area4340 Å2
MethodPISA
4
D: CAP-Gly domain-containing linker protein 1
H: SLAIN motif-containing protein 2


Theoretical massNumber of molelcules
Total (without water)9,0242
Polymers9,0242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-5 kcal/mol
Surface area4580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)38.210, 45.740, 49.360
Angle α, β, γ (deg.)100.06, 105.76, 108.39
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
CAP-Gly domain-containing linker protein 1 / Cytoplasmic linker protein 1 / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg ...Cytoplasmic linker protein 1 / Cytoplasmic linker protein 170 alpha-2 / CLIP-170 / Reed-Sternberg intermediate filament-associated protein / Restin


Mass: 8050.129 Da / Num. of mol.: 4 / Fragment: CAP-Gly 1 domain, residues 56-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CLIP-170 / Plasmid: pDEST17-OI / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: P30622
#2: Protein/peptide
SLAIN motif-containing protein 2


Mass: 974.027 Da / Num. of mol.: 4 / Fragment: C-terminal domain, residues 574-581 / Source method: obtained synthetically / Details: polypeptide synthesis / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9P270
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 288 / 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: 2.09 Å3/Da / Density % sol: 41.2 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.5
Details: 36% PEG 6000, 100mM citric acid, pH 4.5, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→45.54 Å / Num. obs: 28615 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 22.172 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 17.56
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.75-1.80.340.3494.9113823236922540.38295.1
1.8-1.90.2420.2716.1824410410939210.29695.4
1.9-20.1620.1848.8819676326331380.20196.2
2-2.10.1110.13111.6916288268925930.14396.4
2.1-2.50.070.08916.4542723697567640.09797
2.5-30.0410.06223.4526145426041500.06897.4
3-40.0250.04733.3420605339433320.05198.2
4-60.020.03936.3510689175517290.04398.5
6-100.0190.03736.0335615885790.0498.5
100.0220.03635.959001571550.0498.7

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHENIXdev_279refinement
PDB_EXTRACT3.1data extraction
RemDAqdata collection
XDSdata reduction
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2E3I

2e3i


Resolution: 1.75→45.536 Å / Occupancy max: 1 / Occupancy min: 0 / SU ML: 0.22 / σ(F): 2 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1999 6.99 %
Rwork0.1801 --
obs0.1836 28601 96.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.339 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 89.93 Å2 / Biso mean: 22.7384 Å2 / Biso min: 5.56 Å2
Baniso -1Baniso -2Baniso -3
1-3.7286 Å2-6.078 Å2-5.5165 Å2
2---4.8617 Å23.135 Å2
3---1.1331 Å2
Refinement stepCycle: LAST / Resolution: 1.75→45.536 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 5 288 2758
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092549
X-RAY DIFFRACTIONf_angle_d1.153445
X-RAY DIFFRACTIONf_chiral_restr0.086341
X-RAY DIFFRACTIONf_plane_restr0.007454
X-RAY DIFFRACTIONf_dihedral_angle_d13.738908
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7501-1.81270.28741960.22192610280696
1.8127-1.88530.26071960.19982605280196
1.8853-1.97110.24862010.19082676287796
1.9711-2.0750.25651960.17432628282496
2.075-2.2050.21772000.16332647284797
2.205-2.37530.23652000.17452668286897
2.3753-2.61430.28212020.18742681288397
2.6143-2.99250.22062000.18892666286698
2.9925-3.76990.21742040.15872717292199
3.7699-45.55120.16962040.172704290899
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)
11.33510.4569-0.51874.18840.69650.38190.1633-0.06620.05010.408-0.188-0.0561-0.0434-0.23640.00220.1062-0.01170.00040.05490.01320.073910.8486-9.7882-1.1894
21.4639-0.15870.65440.9739-0.83681.60890.01550.0064-0.1697-0.03330.07930.1356-0.0792-0.1087-0.06320.09260.0166-0.00370.05890.0040.056313.7991-4.553-10.7861
30.3018-0.1254-0.01473.3021-1.97171.1808-0.05520.1781-0.0709-0.2771-0.0853-0.43570.17570.2450.09020.1130.02550.00980.1287-0.01440.139121.9392-6.6998-13.0959
40.77580.9785-0.6873.9336-3.35513.671-0.12070.1961-0.47190.4882-0.4797-1.1479-0.02640.62640.3920.08350.0133-0.06650.13740.02710.256724.9389-6.7536-6.913
50.76580.8847-0.15271.3625-0.83321.20160.09720.07090.17040.02880.05890.30780.1496-0.1198-0.13910.098-0.00820.00570.07620.04720.13411.1712-9.8484-7.9369
63.37171.6503-1.32592.3773-1.38070.8608-0.0913-0.1567-0.4233-1.5323-0.22190.65130.4190.17910.2720.30420.0087-0.07010.1698-0.05530.285313.2621-16.2297-14.9359
72.20760.66470.23440.8360.32680.7561-0.4215-0.1344-0.0999-0.06790.0859-0.0869-0.2067-0.04810.24320.1447-0.0006-0.00410.09050.02980.169212.1421-23.286912.0592
81.0244-0.07781.01960.9329-0.38651.02-0.03790.0589-0.10560.0450.19080.1529-0.01-0.10410.02170.132-0.0238-0.0330.08360.0420.074115.7269-33.652516.8706
91.13520.3535-0.03012.311-0.2890.0350.02620.32990.0342-0.2748-0.0494-0.08940.05310.0187-0.01270.13220.008-0.00880.13040.01270.100419.3689-34.86667.6334
105.56091.4343-4.95618.3072-5.92967.1459-0.25390.96030.2774-1.4560.44-0.04460.9957-0.927-0.03450.2378-0.0471-0.00530.1503-0.01230.062117.1816-36.48163.7198
110.4297-0.10760.08781.2401-0.40561.8173-0.24350.00850.19370.03020.21850.2708-0.02050.28920.08240.1634-0.0305-0.05320.05340.02810.137917.352-26.47614.8
121.12591.20930.25231.43740.35570.1050.02720.30670.29340.137-0.3084-0.49-0.42061.16380.02580.3356-0.2104-0.14060.35580.08340.496126.9526-27.28612.5338
131.1834-1.3310.83442.2282-0.90614.2537-0.0181-0.0055-0.1451-0.36430.1958-0.49250.48050.59670.03910.06640.02440.05510.1373-0.03180.15385.2501-30.6215-17.254
142.9982-0.58731.63767.57030.45761.9668-0.54910.2814-0.0577-0.12670.47531.0679-0.0939-0.10660.21390.1351-0.0449-0.01710.0813-0.02140.1019-6.2021-35.8599-14.0903
151.03791.00770.54361.10850.20320.66450.2246-0.0376-0.24430.1548-0.021-0.07290.1538-0.0363-0.13060.0946-0.0074-0.04540.08620.01160.09355.1345-26.6753-5.8553
160.50080.47690.10590.40290.14030.40570.03780.01390.0572-0.0202-0.00490.2370.0245-0.14750.02770.06880.03070.00710.098-0.01140.1252-4.0023-22.0533-7.886
171.11340.9050.44980.92530.13651.75580.0521-0.14850.15850.18740.1569-0.05790.1414-0.1302-0.15270.0593-0.0016-0.03290.0642-0.01590.1084-1.7525-30.3378-9.5365
186.12086.15893.28847.38213.96313.58390.1577-0.0358-1.1082-0.906-0.3469-0.49020.8452-0.36280.33310.5615-0.2877-0.06160.34350.05880.341-6.0436-32.2478-2.4614
190.43010.24070.62832.2224-2.31284.3178-0.0960.5712-0.3678-0.1015-0.0188-0.5270.03330.6688-0.22340.09170.02740.07730.2457-0.11020.1311-1.2647-14.32512.1424
201.74090.5562-1.05356.75770.4541.88480.17520.05040.14680.7622-0.0883-0.52430.00790.0922-0.07220.1088-0.0259-0.02330.0713-0.00190.0691-2.5516-5.056218.7981
210.62520.1850.59810.19870.06620.61010.01420.0863-0.0004-0.02720.06030.02990.03310.1856-0.0510.1268-0.0094-0.03050.12010.00120.0754-12.5619-9.247614.0794
221.7320.7601-0.36173.31040.76141.3978-0.1126-0.2430.19250.5574-0.0660.2982-0.0642-0.14910.07410.08310.02870.04480.0950.00550.0767-18.8351-11.732818.6447
231.18070.5214-0.02511.02940.21590.4538-0.22160.10220.09850.06860.0532-0.0016-0.1314-0.0930.09830.1127-0.0101-0.01250.1068-0.01690.0964-8.4779-6.46916.4036
241.770.70371.47840.35370.56314.0839-0.63620.4150.5873-0.1663-0.0352-0.0637-1.930.25230.70490.6431-0.1264-0.27540.19410.13360.4639-13.11651.819515.0167
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 57:74)A57 - 74
2X-RAY DIFFRACTION2(chain A and resid 75:94)A75 - 94
3X-RAY DIFFRACTION3(chain A and resid 95:108)A95 - 108
4X-RAY DIFFRACTION4(chain A and resid 109:113)A109 - 113
5X-RAY DIFFRACTION5(chain A and resid 114:126)A114 - 126
6X-RAY DIFFRACTION6(chain E and resid 574:581)E574 - 581
7X-RAY DIFFRACTION7(chain B and resid 57:70)B57 - 70
8X-RAY DIFFRACTION8(chain B and resid 71:89)B71 - 89
9X-RAY DIFFRACTION9(chain B and resid 90:108)B90 - 108
10X-RAY DIFFRACTION10(chain B and resid 109:114)B109 - 114
11X-RAY DIFFRACTION11(chain B and resid 115:127)B115 - 127
12X-RAY DIFFRACTION12(chain F and resid 574:581)F574 - 581
13X-RAY DIFFRACTION13(chain C and resid 57:64)C57 - 64
14X-RAY DIFFRACTION14(chain C and resid 65:71)C65 - 71
15X-RAY DIFFRACTION15(chain C and resid 72:88)C72 - 88
16X-RAY DIFFRACTION16(chain C and resid 89:111)C89 - 111
17X-RAY DIFFRACTION17(chain C and resid 112:127)C112 - 127
18X-RAY DIFFRACTION18(chain G and resid 575:581)G575 - 581
19X-RAY DIFFRACTION19(chain D and resid 56:63)D56 - 63
20X-RAY DIFFRACTION20(chain D and resid 64:74)D64 - 74
21X-RAY DIFFRACTION21(chain D and resid 75:97)D75 - 97
22X-RAY DIFFRACTION22(chain D and resid 98:111)D98 - 111
23X-RAY DIFFRACTION23(chain D and resid 112:127)D112 - 127
24X-RAY DIFFRACTION24(chain H and resid 574:581)H574 - 581

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