[English] 日本語
Yorodumi
- PDB-3fso: Crystal structure of the Calx-beta domain of integrin beta4, calc... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3fso
TitleCrystal structure of the Calx-beta domain of integrin beta4, calcium soak
ComponentsIntegrin beta-4
KeywordsCELL ADHESION / Immunoglobulin fold / integrin / Alternative splicing / Disease mutation / Epidermolysis bullosa / Glycoprotein / Membrane / Phosphoprotein / Polymorphism / Receptor / Transmembrane
Function / homology
Function and homology information


trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation ...trophoblast cell migration / Type I hemidesmosome assembly / hemidesmosome assembly / nail development / hemidesmosome / peripheral nervous system myelin formation / skin morphogenesis / Laminin interactions / filopodium assembly / mesodermal cell differentiation / integrin complex / Assembly of collagen fibrils and other multimeric structures / cell adhesion mediated by integrin / Syndecan interactions / cell leading edge / basement membrane / basal plasma membrane / cell-matrix adhesion / G protein-coupled receptor binding / integrin-mediated signaling pathway / cell motility / autophagy / cell-cell adhesion / response to wounding / integrin binding / cell junction / nuclear membrane / receptor complex / cell adhesion / focal adhesion / nucleolus / cell surface / extracellular exosome / metal ion binding / plasma membrane
Similarity search - Function
Integrin beta-4 subunit / CalX-beta domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail ...Integrin beta-4 subunit / CalX-beta domain / Na-Ca exchanger/integrin-beta4 / Calx-beta domain / Domains in Na-Ca exchangers and integrin-beta4 / CalX-like domain superfamily / Integrin beta, epidermal growth factor-like domain 1 / Integrin beta epidermal growth factor like domain 1 / Integrin beta tail domain / Integrin beta subunit, tail / Integrin beta tail domain superfamily / Integrin_B_tail / Integrin beta subunit, VWA domain / Integrin beta subunit / Integrin beta N-terminal / Integrin beta chain VWA domain / Integrin plexin domain / Integrins beta chain cysteine-rich domain signature. / Integrin beta subunits (N-terminal portion of extracellular region) / EGF-like domain, extracellular / EGF-like domain / PSI domain / domain found in Plexins, Semaphorins and Integrins / von Willebrand factor A-like domain superfamily / EGF-like domain signature 2. / Fibronectin type III domain / EGF-like domain signature 1. / EGF-like domain / Fibronectin type 3 domain / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.405 Å
AuthorsAlonso-Garcia, N. / Ingles-Prieto, A. / de Pereda, J.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: Structure of the Calx-beta domain of the integrin beta4 subunit: insights into function and cation-independent stability
Authors: Alonso-Garcia, N. / Ingles-Prieto, A. / Sonnenberg, A. / de Pereda, J.M.
History
DepositionJan 11, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Integrin beta-4
B: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)27,9332
Polymers27,9332
Non-polymers00
Water5,513306
1
A: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)13,9671
Polymers13,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Integrin beta-4


Theoretical massNumber of molelcules
Total (without water)13,9671
Polymers13,9671
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.310, 51.650, 87.430
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Integrin beta-4 / GP150


Mass: 13966.667 Da / Num. of mol.: 2 / Fragment: Calx-beta domain, residues 989-1107
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITGB4 / Plasmid: Modified pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P16144
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / 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: 2.03 Å3/Da / Density % sol: 39.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.3
Details: 50mM Tris-HCl, 26% PEG 1500; CRYSTAL WAS SOAKED IN 50mM Tris-HCl, 25% PEG 1500, 10mM CaCl2 PRIOR TO DATA COLLECTION, pH 8.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Aug 5, 2007
RadiationMonochromator: HELIOS OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.4→22 Å / Num. all: 44715 / Num. obs: 44715 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Biso Wilson estimate: 9.93 Å2 / Net I/σ(I): 20.5
Reflection shellResolution: 1.4→1.5 Å / Redundancy: 10.7 % / Mean I/σ(I) obs: 9.9 / % possible all: 91.1

-
Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHENIX(phenix.refine)model building
PHENIX(phenix.refine)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3FQ4

3fq4


Resolution: 1.405→21.858 Å / Occupancy max: 1 / Occupancy min: 0.25 / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2115 2229 4.99 %RANDOM
Rwork0.182 42471 --
all0.1835 44700 --
obs0.1835 44700 99.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 73.366 Å2 / ksol: 0.505 e/Å3
Displacement parametersBiso max: 146.08 Å2 / Biso mean: 19.254 Å2 / Biso min: 5.92 Å2
Baniso -1Baniso -2Baniso -3
1--2.7095 Å20 Å20 Å2
2---1.0226 Å20 Å2
3----3.3249 Å2
Refinement stepCycle: LAST / Resolution: 1.405→21.858 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3803 0 0 308 4111
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073852
X-RAY DIFFRACTIONf_angle_d0.9096983
X-RAY DIFFRACTIONf_chiral_restr0.071282
X-RAY DIFFRACTIONf_plane_restr0.005632
X-RAY DIFFRACTIONf_dihedral_angle_d15.5371008
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.405-1.4360.2381250.2232397252290
1.436-1.4690.261280.22926302758100
1.469-1.5060.2341540.20626202774100
1.506-1.5460.2521400.19126252765100
1.546-1.5920.2161270.17826592786100
1.592-1.6430.1981370.17126672804100
1.643-1.7020.2211440.16726352779100
1.702-1.770.2011360.16226712807100
1.77-1.8510.1991370.1626862823100
1.851-1.9480.2391380.2162645278399
1.948-2.070.2011420.17626592801100
2.07-2.230.1711420.1626542796100
2.23-2.4540.2411490.20826842833100
2.454-2.8090.221400.16427252865100
2.809-3.5360.1911410.15727352876100
3.536-21.860.2031490.1882779292897
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)
10.0145-0.00140.01510.0170.0068-0.00120.15150.0976-0.0473-0.277-0.10590.3704-0.14070.0072-0.00010.1988-0.0032-0.01750.1384-0.00930.114124.137233.1811.6738
20.15110.13840.18190.3342-0.0111.01030.1478-0.03010.2222-0.04810.07740.14490.0434-0.27770.0490.1058-0.0048-0.00110.1312-0.01690.091817.992326.431218.2837
3-0.0186-0.00850.021-0.0161-0.02430.033-0.27060.30040.24660.1298-0.3111-0.30840.2083-0.07510.00010.17560.00550.00490.14280.02290.160820.374218.180131.4281
40.05010.75590.42220.5260.48250.1230.0763-0.01310.029-0.0621-0.02920.07970.1313-0.17310.00670.10550.01180.00410.1049-0.00340.087423.891421.540317.3218
50.0337-0.0048-0.0066-0.0025-0.00610.04440.030.2582-0.1688-0.0695-0.02140.1483-0.13130.096700.2536-0.0106-0.00540.2189-0.01120.107925.992428.0862-1.2809
60.08350.31750.02910.3372-0.09770.05780.04990.03360.0252-0.0218-0.0416-0.0264-0.07250.0109-00.1258-0.00290.0230.157-0.01810.094331.751931.290916.3856
70.0020.0030.04230.0341-0.00320.0279-0.0008-0.07170.03390.27510.0438-0.0343-0.24080.0298-00.1197-0.00440.02730.0959-0.01250.106726.83529.345635.5088
80.1959-0.0310.214-0.013-0.0226-0.06060.16810.4947-0.1543-0.0058-0.20790.107-0.45060.3845-0.00250.1166-0.01810.00860.1851-0.01820.113732.216927.077627.8108
9-0.0013-0.01740.0140.0006-0.01870.03260.1883-0.2159-0.07260.0186-0.1218-0.1480.2338-0.1998-0.00030.113-0.0010.00940.1762-0.01460.105834.838227.67313.6292
100.0440.00110.11730.0533-0.05910.0467-0.2597-0.0791-0.394-0.10630.1217-0.21760.20370.028-0.00050.12190.00850.03890.1515-0.0170.134429.786121.83146.7842
11-0.1616-0.00920.03530.0609-0.05520.0579-0.05850.1316-0.11670.05050.015-0.03110.3223-0.0424-0.00010.1544-0.0010.00120.1439-0.01310.087428.16120.292525.4739
12-0.0003-0.11720.1110.1034-0.007-0.02040.4236-0.19430.01310.6129-0.04760.52960.09050.20590.05580.47860.05460.12630.2082-0.01890.1222.19420.078139.2905
130.093-0.0948-0.1949-0.24590.10820.10410.0541-0.40660.05070.2837-0.11190.1174-0.23180.2659-0.15340.1531-0.01350.03990.16-0.0190.085420.302629.068531.6437
14-0.00030.02690.01690.1810.12540.0450.0339-0.215-0.08270.0113-0.1328-0.0939-0.33760.2139-0.00020.1425-0.0190.03470.141-0.00940.091728.884834.656516.4026
150.13450.01040.0499-0.0091-0.01250.0217-0.1780.0498-0.0089-0.2637-0.0781-0.1278-0.30960.27850.00070.1883-0.03840.0410.22620.00980.135133.860434.0595.6024
16-0.3175-0.0874-0.40280.27850.162-0.0010.019-0.01950.08490.01080.02870.0896-0.1573-0.300600.11140.0250.01610.14210.00610.102120.900432.558317.4053
170.2098-0.0724-0.0663-0.03490.3620.547-0.1081-0.0267-0.260.72290.38470.35790.4940.01260.02470.28880.01550.04970.06070.06570.223316.350820.587734.5573
180.02370.04510.00090.0318-0.02370.01270.1474-0.2475-0.0924-0.0467-0.16190.07370.00680.11020.00010.11370.00030.03010.23830.0150.111645.175911.180220.2388
190.43230.05780.11460.14920.20130.10570.043-0.0798-0.12010.08530.0043-0.05010.125-0.11740.01710.0899-0.01980.01590.08980.00460.087239.23865.95524.6072
200.05970.00890.02740.12280.0152-0.01050.41150.3901-0.1464-0.0378-0.6609-0.061-0.0431-0.11440.00020.10020.0678-0.00580.2253-0.00460.141832.15196.5359-9.4231
210.43380.037-0.35350.1957-0.00220.1982-0.0132-0.0553-0.05090.0549-0.01150.1170.039-0.0791-00.079-0.00240.00610.11420.00620.093134.032911.37574.4785
220.0566-0.108-0.0137-0.09640.02180.0145-0.0716-0.53820.32630.38770.1351-0.0749-0.14990.395-0.08460.14810.04250.01680.2148-0.03960.04840.247217.560719.924
230.3470.44330.16220.53550.03430.3822-0.1369-0.06170.0508-0.0753-0.08390.09830.13480.0262-0.26080.07470.0041-0.00560.06640.00430.057845.043617.0404-0.0909
240.6593-0.30390.40790.1779-0.16560.3385-0.04990.22580.1509-0.06680.0224-0.1691-0.10040.1629-0.02570.0862-0.01330.01020.101-0.00440.10141.386114.2534-12.5516
250.1811-0.01280.1003-0.03520.0842-0.1096-0.4218-0.02650.0648-0.1312-0.00920.1455-0.23230.0512-0.00050.12190.0043-0.03560.0890.00680.091241.73522.21471.8254
260.0716-0.14410.05450.047-0.11790.13620.0352-0.09980.0970.05510.03420.2556-0.0034-0.14390.0050.10310.03020.03480.1568-0.0110.11334.391717.863515.4176
270.06050.1103-0.00150.01190.1060.051-0.15970.10790.06930.1616-0.0549-0.0105-0.4501-0.3178-00.13810.01680.00790.09850.01120.118633.271216.42991.0803
28-0.03780.02210.03130.02450.0032-0.00090.15390.4488-0.0865-0.595-0.0893-0.270.2954-0.5278-0.00030.1799-0.0081-0.0090.2823-0.03350.064931.895413.998-14.9676
29-0.013-0.00490.01850.00230.03680.0105-0.15931.1546-0.18280.14310.01650.3539-0.1238-0.53760.0010.175-0.0765-0.01590.4552-0.07840.201534.12641.6525-19.5995
300.6651-0.3379-0.1626-0.01750.04320.1528-0.07930.04230.0382-0.02660.0060.0435-0.0180.2367-0.07630.0909-0.0099-0.00030.0934-0.00670.076544.807112.8932-0.557
310.0248-0.03160.01650.08870.01260.00420.1948-0.10290.1698-0.0956-0.3522-0.08130.01560.48950.00040.1255-0.01660.01420.2398-0.07330.132446.170620.898616.4143
320.05040.01740.0160.02630.01160.0125-0.0884-0.37010.0328-0.15840.2047-0.16140.12880.25340.00050.0925-0.00670.00960.163-0.00880.104747.5469.740412.4411
330.2106-0.0194-0.23630.0029-0.01150.0996-0.06060.12110.06920.01040.0114-0.0474-0.07710.127900.0911-0.00580.00220.09140.00160.09242.15037.2411-0.7847
340.3694-0.1641-0.60970.57871.1090.88230.3672-0.0036-0.3655-0.2474-0.5234-0.3798-0.2826-0.46910.03560.0811-0.0407-0.05230.2588-0.08090.163531.39232.4107-13.0531
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 988:991)
2X-RAY DIFFRACTION2chain A and resid 992:1000)
3X-RAY DIFFRACTION3chain A and resid 1001:1005)
4X-RAY DIFFRACTION4chain A and resid 1006:1015)
5X-RAY DIFFRACTION5chain A and resid 1016:1019)
6X-RAY DIFFRACTION6chain A and resid 1020:1029)
7X-RAY DIFFRACTION7chain A and resid 1030:1038)
8X-RAY DIFFRACTION8chain A and resid 1039:1043)
9X-RAY DIFFRACTION9chain A and resid 1044:1047)
10X-RAY DIFFRACTION10chain A and resid 1048:1055)
11X-RAY DIFFRACTION11chain A and resid 1056:1062)
12X-RAY DIFFRACTION12chain A and resid 1063:1075)
13X-RAY DIFFRACTION13chain A and resid 1076:1080)
14X-RAY DIFFRACTION14chain A and resid 1081:1086)
15X-RAY DIFFRACTION15chain A and resid 1087:1090)
16X-RAY DIFFRACTION16chain A and resid 1091:1101)
17X-RAY DIFFRACTION17chain A and resid 1102:1105)
18X-RAY DIFFRACTION18chain B and resid 988:991)
19X-RAY DIFFRACTION19chain B and resid 992:999)
20X-RAY DIFFRACTION20chain B and resid 1000:1003)
21X-RAY DIFFRACTION21chain B and resid 1004:1016)
22X-RAY DIFFRACTION22chain B and resid 1017:1023)
23X-RAY DIFFRACTION23chain B and resid 1024:1029)
24X-RAY DIFFRACTION24chain B and resid 1030:1040)
25X-RAY DIFFRACTION25chain B and resid 1041:1046)
26X-RAY DIFFRACTION26chain B and resid 1047:1054)
27X-RAY DIFFRACTION27chain B and resid 1055:1060)
28X-RAY DIFFRACTION28chain B and resid 1061:1064)
29X-RAY DIFFRACTION29chain B and resid 1071:1076)
30X-RAY DIFFRACTION30chain B and resid 1077:1086)
31X-RAY DIFFRACTION31chain B and resid 1087:1090)
32X-RAY DIFFRACTION32chain B and resid 1091:1094)
33X-RAY DIFFRACTION33chain B and resid 1095:1102)
34X-RAY DIFFRACTION34chain B and resid 1103:1106)

+
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://pdbjlvh1.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