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- PDB-7asc: TGFBIp mutant A546T -

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Basic information

Entry
Database: PDB / ID: 7asc
TitleTGFBIp mutant A546T
ComponentsTransforming growth factor-beta-induced protein ig-h3
KeywordsPROTEIN FIBRIL / granular corneal dystrophy / lattice corneal dystrophy / protein aggregation / extracellular matrix protein
Function / homology
Function and homology information


negative regulation of cell adhesion / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / chondrocyte differentiation / collagen binding / cell adhesion molecule binding / extracellular matrix organization / visual perception / extracellular matrix ...negative regulation of cell adhesion / extracellular matrix binding / extracellular matrix structural constituent / basement membrane / chondrocyte differentiation / collagen binding / cell adhesion molecule binding / extracellular matrix organization / visual perception / extracellular matrix / trans-Golgi network / integrin binding / : / angiogenesis / cell population proliferation / cell adhesion / Amyloid fiber formation / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
TGF beta-induced protein/periostin / EMI domain / EMI domain profile. / : / Fasciclin domain / Four repeated domains in the Fasciclin I family of proteins, present in many other contexts. / FAS1 domain / FAS1 domain superfamily / FAS1/BIgH3 domain profile.
Similarity search - Domain/homology
Transforming growth factor-beta-induced protein ig-h3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.8 Å
AuthorsAndersen, G.R. / Nielsen, N.S. / Gadeberg, T.A.F.
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Mutation-induced dimerization of transforming growth factor-beta-induced protein may drive protein aggregation in granular corneal dystrophy.
Authors: Nielsen, N.S. / Gadeberg, T.A.F. / Poulsen, E.T. / Harwood, S.L. / Weberskov, C.E. / Pedersen, J.S. / Andersen, G.R. / Enghild, J.J.
History
DepositionOct 27, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 23, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 31, 2024Group: 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_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming growth factor-beta-induced protein ig-h3
B: Transforming growth factor-beta-induced protein ig-h3


Theoretical massNumber of molelcules
Total (without water)130,2472
Polymers130,2472
Non-polymers00
Water00
1
A: Transforming growth factor-beta-induced protein ig-h3


Theoretical massNumber of molelcules
Total (without water)65,1231
Polymers65,1231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transforming growth factor-beta-induced protein ig-h3


Theoretical massNumber of molelcules
Total (without water)65,1231
Polymers65,1231
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)206.760, 206.760, 127.540
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: GLN / End label comp-ID: GLN / Auth seq-ID: 46 - 633 / Label seq-ID: 2 - 589

Dom-IDComponent-IDSelection detailsAuth asym-IDLabel asym-ID
11chain 'A'AA
22chain 'B'BB

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Components

#1: Protein Transforming growth factor-beta-induced protein ig-h3 / Beta ig-h3 / Kerato-epithelin / RGD-containing collagen-associated protein / RGD-CAP


Mass: 65123.363 Da / Num. of mol.: 2 / Mutation: A546T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBI, BIGH3 / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q15582
Has protein modificationY

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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: 5.23 Å3/Da / Density % sol: 76.49 %
Crystal growTemperature: 292 K / Method: vapor diffusion / pH: 9
Details: 25 mM BIS-TRIS propane pH 9.0, 5% v/v PEG-mme 550, 1% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 4.8→80.31 Å / Num. obs: 14000 / % possible obs: 99.7 % / Redundancy: 13 % / Biso Wilson estimate: 279.5 Å2 / CC1/2: 0.999 / CC star: 1 / Rmerge(I) obs: 0.1385 / Net I/σ(I): 11.1
Reflection shellResolution: 4.8→4.973 Å / Rmerge(I) obs: 2.9 / Num. unique obs: 1376 / CC1/2: 0.39

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5nv6

5nv6


Resolution: 4.8→80.31 Å / SU ML: 0.8391 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 33.0194
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2587 1400 10.01 %
Rwork0.25 12585 -
obs0.251 13985 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 332.11 Å2
Refinement stepCycle: LAST / Resolution: 4.8→80.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9022 0 0 0 9022
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00699168
X-RAY DIFFRACTIONf_angle_d1.411612448
X-RAY DIFFRACTIONf_chiral_restr0.07611488
X-RAY DIFFRACTIONf_plane_restr0.00781604
X-RAY DIFFRACTIONf_dihedral_angle_d12.06195610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.8-4.970.37151380.36761240X-RAY DIFFRACTION100
4.97-5.170.38391360.36141229X-RAY DIFFRACTION99.93
5.17-5.410.36641380.36021242X-RAY DIFFRACTION99.86
5.41-5.690.35421360.35161227X-RAY DIFFRACTION100
5.69-6.050.3611390.33311242X-RAY DIFFRACTION100
6.05-6.510.33881390.34891252X-RAY DIFFRACTION99.93
6.51-7.170.30951400.33251259X-RAY DIFFRACTION100
7.17-8.210.27981400.27551262X-RAY DIFFRACTION99.72
8.21-10.340.26561430.22341284X-RAY DIFFRACTION99.93
10.34-80.310.18631510.18271348X-RAY DIFFRACTION98.17
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)
15.45836188221.624540597470.8927485419633.1243807891.962836736088.25440661917-1.543630037371.008276124861.0929236871.77368583116-0.7740616386171.328530623661.722198175330.3038341049771.316061242413.400706928650.1743710861810.03662227868453.299574930380.8496462485052.96529761936196.00054670370.373843115416.0287731601
29.694464274220.9442276972374.8139012227711.48143846494.1637379244211.43834201960.357134831943-1.730586864020.761740852588-0.1787230129631.09935865865-0.0986633876792-0.199419757705-0.961436810472-1.555495361543.339319772130.311779018820.339891147882.817913822560.2436304224563.18184871418205.84564269864.931571450536.0715747308
312.4676560148-5.24933776157-0.1277573281019.434050374822.489197962345.37051616593-0.926677399295-0.15674054230.02324774253430.2042310459250.0534510811990.1096813501630.08493691007640.6294064576430.7199732840653.289245855770.1475547963730.1828615031082.973870412570.2276676134723.07106841479227.1436376452.147135583418.7604667917
45.178854939524.24543919899-2.34268317526-2.67759493878-1.656037855467.81459788554-0.0240519075110.207540452189-0.199656467022-0.3071113289120.16412578415-0.367536087599-0.8095579804471.78140125956-0.2489322943653.803059889850.3748698832550.2649272627982.923724895210.13730807763.4566813212240.4250599150.6723069151-10.2524629834
51.659192875860.9198437251754.028415842060.06178674073253.06061536278.29098780043-0.920896615671.911651594250.0555311316484-1.734551774550.803941199937-1.52280719226-0.874819978338-0.0629540760003-0.08750577609744.972541604750.1794739964840.629498928634.793779545220.1287510756273.77305960495244.01290244364.6970186857-38.0066514599
63.62838941452-5.18706894960.800848249293.907152698420.6332176455253.62823387644-0.464023661115-0.639842290982-1.800185892810.546545055567-0.7993453016190.542480225462.327318681821.871182061261.307543481843.873481297830.02852269012090.01157245798543.406118201250.6402372186133.54225732405227.21851193288.4481546012-10.9052619713
79.71413457804-3.651423072482.0755962197912.04808511882.8271295067510.3125467595-0.491671731847-0.2921867349290.581941687808-0.622287811548-0.20658312669-0.4075650432921.328220505960.4334448500940.6489085975143.269894790460.08195050229880.3174591318183.074935748870.0648303995353.45671489074247.32407105782.5475034602-1.1287709393
87.156534946131.77591715246-0.992893476329.016325066553.9605371318310.32538668690.4608332460250.313954381551-0.0442170861022-1.368549872150.602135343335-0.3992176091830.407975379913-0.60825398285-1.077533715812.864665743180.2767607169750.1561187077332.9001706508-0.07711022967633.23895750835234.3488673892.157992493924.5304378704
98.764173331290.191059377554-2.59615051104-0.137727501179-2.035878260036.13622185504-0.735053086761-1.304129650290.0439484816408-0.1297929045960.6607873613770.287654613984-0.3898169901770.3385920048780.07254979850823.070602268860.1914307130550.2944941743683.09149472706-0.07604706900833.21919799415207.58261213898.613850812140.8232427251
101.261003402954.438990912-1.98721386424-0.6062323327131.769663407895.916351793141.01011992018-0.1346432863131.285880373631.22430205807-1.543152521453.769976280631.61490815592-1.76237834050.830244609993.997883603350.5533991445410.5344608007253.711987692670.01782622695744.24754539917176.76133021593.674655130343.4573523051
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resid 45:101
2X-RAY DIFFRACTION2chain A and resid 102:239
3X-RAY DIFFRACTION3chain A and resid 240:367
4X-RAY DIFFRACTION4chain A and resid 368:500
5X-RAY DIFFRACTION5chain A and resid 501:633
6X-RAY DIFFRACTION6chain B and resid 45:101
7X-RAY DIFFRACTION7chain B and resid 102:239
8X-RAY DIFFRACTION8chain B and resid 240:367
9X-RAY DIFFRACTION9chain B and resid 368:500
10X-RAY DIFFRACTION10chain B and resid 501:633

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