[English] 日本語
Yorodumi
- PDB-3rdv: Structure of the SLAIN2c-CLIPCG1 complex -

+
Open data


ID or keywords:

Loading...

-
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 / Signaling by LTK in cancer / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ruffle / cytoplasmic microtubule organization / positive regulation of microtubule polymerization ...microtubule nucleation / microtubule plus-end binding / microtubule bundle formation / Signaling by LTK in cancer / intermediate filament / RHO GTPases activate IQGAPs / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / ruffle / cytoplasmic microtubule organization / positive regulation of microtubule polymerization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / tubulin binding / cytoplasmic vesicle membrane / Resolution of Sister Chromatid Cohesion / RHO GTPases Activate Formins / kinetochore / Separation of Sister Chromatids / mitotic cell cycle / microtubule cytoskeleton / cell cortex / microtubule binding / microtubule / centrosome / zinc ion binding / identical protein binding / nucleus / plasma membrane / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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


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


Mass: 18.015 Da / Num. of mol.: 288 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more