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- PDB-7c3m: Structure of FERM protein -

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Basic information

Entry
Database: PDB / ID: 7c3m
TitleStructure of FERM protein
ComponentsFermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3
KeywordsSIGNALING PROTEIN / FERM Protein / Kindlin / Integrin
Function / homology
Function and homology information


cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / cell projection / integrin-mediated signaling pathway ...cell-substrate junction / regulation of cell-cell adhesion mediated by integrin / integrin activation / podosome / leukocyte cell-cell adhesion / substrate adhesion-dependent cell spreading / cell-matrix adhesion / platelet alpha granule lumen / cell projection / integrin-mediated signaling pathway / platelet aggregation / integrin binding / Platelet degranulation / positive regulation of cell migration / lipid binding / extracellular exosome / extracellular region / membrane
Similarity search - Function
Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues ...Kindlin/fermitin, PH domain / Kindlin/fermitin / Kindlin-2, N-terminal / Kindlin-2 N-terminal domain / FERM domain signature 2. / FERM central domain / FERM central domain / FERM superfamily, second domain / Band 4.1 domain / Band 4.1 homologues / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain / PH-like domain superfamily
Similarity search - Domain/homology
Fermitin family homolog 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.6 Å
AuthorsBu, W. / Loh, Z.Y. / Jin, S. / Basu, S. / Ero, R. / Park, J.E. / Yan, X. / Wang, M. / Sze, S.K. / Tan, S.M. / Gao, Y.G.
Funding support Singapore, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Singapore)MOE2017-T2-1-106 Singapore
CitationJournal: Plos Biol. / Year: 2020
Title: Structural basis of human full-length kindlin-3 homotrimer in an auto-inhibited state.
Authors: Bu, W. / Levitskaya, Z. / Loh, Z.Y. / Jin, S. / Basu, S. / Ero, R. / Yan, X. / Wang, M. / Ngan, S.F.C. / Sze, S.K. / Tan, S.M. / Gao, Y.G.
History
DepositionMay 13, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 22, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3
B: Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3
C: Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)229,3883
Polymers229,3883
Non-polymers00
Water0
1
A: Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)76,4631
Polymers76,4631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)76,4631
Polymers76,4631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3


Theoretical massNumber of molelcules
Total (without water)76,4631
Polymers76,4631
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.760, 204.620, 269.950
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Fermitin family homolog 3,Fermitin family homolog 3,Fermitin family homolog 3 / Kindlin-3 / MIG2-like protein / Unc-112-related protein 2


Mass: 76462.750 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FERMT3, KIND3, MIG2B, URP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86UX7
Sequence detailsThe authors know the sequence of Residues 309-349, EVGEPAGTDPGLDDLDVALSNLEVKLEGSAPTDVLDSLTTI but ...The authors know the sequence of Residues 309-349, EVGEPAGTDPGLDDLDVALSNLEVKLEGSAPTDVLDSLTTI but don't know how the coordinates align with the sequence due to poor electron density. The UNK residue numbers are meaningless.

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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: 3.62 Å3/Da / Density % sol: 66.02 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop
Details: 3M sodium formate pH 7.0, 3% w/v xylitol, and 9% glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 37501 / % possible obs: 99.9 % / Redundancy: 22.4 % / CC1/2: 0.999 / Net I/σ(I): 14.7
Reflection shellResolution: 3.6→3.69 Å / Redundancy: 23.5 % / Mean I/σ(I) obs: 0.97 / Num. unique obs: 3704 / CC1/2: 0.547 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998)refinement
XDSdata reduction
XDSdata scaling
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 3.6→49.202 Å / SU ML: 0.55 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 34.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3167 1770 4.73 %
Rwork0.305 --
obs0.3055 37450 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.6→49.202 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13538 0 0 0 13538
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00413853
X-RAY DIFFRACTIONf_angle_d0.95718796
X-RAY DIFFRACTIONf_dihedral_angle_d12.3868333
X-RAY DIFFRACTIONf_chiral_restr0.0492051
X-RAY DIFFRACTIONf_plane_restr0.0062445
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6001-3.69740.39861390.39772682X-RAY DIFFRACTION100
3.6974-3.80620.39481520.37022693X-RAY DIFFRACTION100
3.8062-3.9290.37511420.36472702X-RAY DIFFRACTION100
3.929-4.06930.33391650.35362674X-RAY DIFFRACTION100
4.0693-4.23220.34411280.3452714X-RAY DIFFRACTION100
4.2322-4.42470.33711210.32292735X-RAY DIFFRACTION100
4.4247-4.65780.30781330.31482766X-RAY DIFFRACTION100
4.6578-4.94940.35741180.31542729X-RAY DIFFRACTION100
4.9494-5.33110.30691240.33292773X-RAY DIFFRACTION100
5.3311-5.86680.32481570.34282734X-RAY DIFFRACTION100
5.8668-6.71390.3451370.33892758X-RAY DIFFRACTION100
6.7139-8.45190.28361320.30312815X-RAY DIFFRACTION100
8.4519-49.20.28791220.2472905X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -17.2247 Å / Origin y: 204.2496 Å / Origin z: 306.9721 Å
111213212223313233
T1.5244 Å20.026 Å20.0333 Å2-1.5781 Å2-0.1081 Å2--1.7555 Å2
L0.3167 °20.027 °20.0363 °2-0.0992 °2-0.2542 °2--0.2469 °2
S-0.0649 Å °-0.0098 Å °0.0873 Å °-0.0434 Å °-0.0045 Å °0.089 Å °-0.0179 Å °-0.0596 Å °0.0721 Å °
Refinement TLS groupSelection details: all

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