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- PDB-5vqf: Crystal Structure of pro-TGF-beta 1 -

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Basic information

Entry
Database: PDB / ID: 5vqf
TitleCrystal Structure of pro-TGF-beta 1
ComponentsTransforming growth factor beta-1
KeywordsPROTEIN BINDING / pro-complex / latency / homodimer
Function / homology
Function and homology information


Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity ...Platelet degranulation / Cell surface interactions at the vascular wall / Molecules associated with elastic fibres / TGF-beta receptor signaling activates SMADs / Syndecan interactions / RUNX3 regulates CDKN1A transcription / RUNX3 regulates p14-ARF / Downregulation of TGF-beta receptor signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Regulation of RUNX3 expression and activity / regulation of binding / regulation of DNA binding / positive regulation of microglia differentiation / negative regulation of skeletal muscle tissue development / regulation of striated muscle tissue development / regulation of protein import into nucleus / type III transforming growth factor beta receptor binding / negative regulation of hyaluronan biosynthetic process / extracellular matrix assembly / negative regulation of macrophage cytokine production / odontoblast differentiation / positive regulation of isotype switching to IgA isotypes / membrane protein intracellular domain proteolysis / hyaluronan catabolic process / regulation of transforming growth factor beta receptor signaling pathway / ATP biosynthetic process / receptor catabolic process / type II transforming growth factor beta receptor binding / positive regulation of chemotaxis / type I transforming growth factor beta receptor binding / negative regulation of myoblast differentiation / cell-cell junction organization / response to cholesterol / positive regulation of fibroblast migration / phosphate-containing compound metabolic process / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of cell-cell adhesion / negative regulation of fat cell differentiation / positive regulation of interleukin-17 production / positive regulation of SMAD protein signal transduction / negative regulation of blood vessel endothelial cell migration / positive regulation of cell division / negative regulation of cell cycle / positive regulation of collagen biosynthetic process / positive regulation of blood vessel endothelial cell migration / epithelial to mesenchymal transition / lymph node development / chondrocyte differentiation / hematopoietic progenitor cell differentiation / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / extrinsic apoptotic signaling pathway / positive regulation of protein dephosphorylation / cellular response to transforming growth factor beta stimulus / positive regulation of protein metabolic process / transforming growth factor beta receptor signaling pathway / extracellular matrix / positive regulation of superoxide anion generation / negative regulation of protein phosphorylation / cytokine activity / response to progesterone / positive regulation of protein secretion / antigen binding / growth factor activity / positive regulation of protein-containing complex assembly / negative regulation of cell growth / response to wounding / positive regulation of protein import into nucleus / negative regulation of epithelial cell proliferation / response to estradiol / regulation of cell population proliferation / positive regulation of ERK1 and ERK2 cascade / blood microparticle / positive regulation of cell migration / inflammatory response / negative regulation of cell population proliferation / protein phosphorylation / negative regulation of gene expression / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / nucleus / cytoplasm
Similarity search - Function
Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2330 / Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family ...Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #2330 / Jelly Rolls - #970 / Transforming growth factor beta-1 proprotein / Transforming growth factor-beta / TGF-beta, propeptide / TGF-beta propeptide / Transforming growth factor beta, conserved site / TGF-beta family signature. / Transforming growth factor-beta-related / Transforming growth factor-beta (TGF-beta) family / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Helix non-globular / Special / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsZhao, B. / Xu, S. / Dong, X. / Lu, C. / Springer, T.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIH/NIAMS)R01AR067288 United States
Citation
Journal: J. Biol. Chem. / Year: 2018
Title: Prodomain-growth factor swapping in the structure of pro-TGF-beta 1.
Authors: Zhao, B. / Xu, S. / Dong, X. / Lu, C. / Springer, T.A.
#1: Journal: Nature / Year: 2011
Title: Latent TGF-beta structure and activation.
Authors: Shi, M. / Zhu, J. / Wang, R. / Chen, X. / Mi, L. / Walz, T. / Springer, T.A.
History
DepositionMay 8, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 15, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Structure summary / Category: citation / entity / struct_ref_seq_dif
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _entity.pdbx_mutation / _struct_ref_seq_dif.details
Revision 1.2Feb 14, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,1657
Polymers165,7304
Non-polymers1,4353
Water00
1
A: Transforming growth factor beta-1
B: Transforming growth factor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,4513
Polymers82,8652
Non-polymers5871
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9340 Å2
ΔGint-61 kcal/mol
Surface area34210 Å2
MethodPISA
2
C: Transforming growth factor beta-1
D: Transforming growth factor beta-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,7144
Polymers82,8652
Non-polymers8492
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9530 Å2
ΔGint-57 kcal/mol
Surface area35750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.660, 126.920, 137.920
Angle α, β, γ (deg.)90.00, 96.70, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Transforming growth factor beta-1 / TGF-beta-1


Mass: 41432.410 Da / Num. of mol.: 4 / Mutation: C4S, N147Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TGFB1 / Plasmid: pEF1-puro
Details (production host): pEF1-puro is derived from pEF1/V5-HisA (Invitrogen) with the neomycin gene replaced with puromycin.
Cell (production host): epithelial / Cell line (production host): CHO-lec3.2.8.1 / Production host: Cricetulus griseus (Chinese hamster) / Tissue (production host): Ovary / References: UniProt: P07200
#2: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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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: 2.86 Å3/Da / Density % sol: 56.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 7% PEG 3350, 17% isopropanol, 0.1m Na citrate pH 5.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 0.97934, 0.97932, 0.97956, 0.95667
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 12, 2009
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979321
30.979561
40.956671
ReflectionResolution: 2.9→50 Å / Num. obs: 39918 / % possible obs: 96.1 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 15.3
Reflection shellResolution: 2.9→2.98 Å / Redundancy: 4.3 % / Rmerge(I) obs: 2.74 / Mean I/σ(I) obs: 0.55 / Num. unique obs: 2994 / CC1/2: 0.33 / % possible all: 98

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
PDB_EXTRACT3.1data extraction
XDSdata processing
SOLVEphasing
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3RJR

3rjr


Resolution: 2.9→37.142 Å / SU ML: 0.64 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.27
RfactorNum. reflection% reflection
Rfree0.2798 1354 3.39 %
Rwork0.2392 --
obs0.2406 39887 96.19 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.9→37.142 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10658 0 95 0 10753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00511030
X-RAY DIFFRACTIONf_angle_d0.84914978
X-RAY DIFFRACTIONf_dihedral_angle_d9.2826792
X-RAY DIFFRACTIONf_chiral_restr0.0511663
X-RAY DIFFRACTIONf_plane_restr0.0051903
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.9-3.00360.51971450.45193877X-RAY DIFFRACTION98
3.0036-3.12380.45841380.40233909X-RAY DIFFRACTION98
3.1238-3.26590.39861370.34133892X-RAY DIFFRACTION98
3.2659-3.4380.29561360.28253949X-RAY DIFFRACTION98
3.438-3.65320.31421350.26393959X-RAY DIFFRACTION98
3.6532-3.9350.27911420.24433907X-RAY DIFFRACTION99
3.935-4.33040.28881320.21653951X-RAY DIFFRACTION99
4.3304-4.95580.23751430.18633955X-RAY DIFFRACTION98
4.9558-6.2390.25911350.22413952X-RAY DIFFRACTION98
6.239-37.14480.27051110.24863182X-RAY DIFFRACTION78
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)
12.84920.25370.92082.16140.01856.5853-0.0969-0.87580.87750.0534-0.09710.4503-2.6584-0.58480.15822.64230.3241-0.14711.75-0.23971.7126-85.009753.6164-15.674
28.1379-1.66342.65873.21831.8787.6055-0.8923-0.88640.39170.39280.71850.2254-0.20940.0492-0.05562.2834-0.059-0.08521.5254-0.12490.9765-78.805843.95960.0816
35.2173-1.97272.52948.00090.00197.3535-0.12610.2334-0.411-0.1863-0.05781.52090.1363-0.66610.40251.4783-0.4343-0.12041.3076-0.17371.1602-78.768625.0745-32.7156
47.05591.20475.70822.2064-0.21646.32890.49770.0027-0.4307-0.23630.0511-0.14450.54690.2607-0.77581.87890.04930.04881.0231-0.0650.9061-68.551818.0155-34.2654
58.9068-0.4457-2.57217.2031-0.96653.84790.2092-1.1894-0.23721.6232-0.0313-1.1227-0.35990.6658-0.36531.7665-0.2213-0.35231.8264-0.20441.0485-57.382924.173-5.8299
66.0694-3.10942.95834.98820.95657.7267-0.35790.3520.95920.1873-0.1-0.5407-1.9688-0.18320.40261.7846-0.2752-0.08881.06020.00551.0398-74.226343.0598-22.9025
72.0107-0.84341.17265.1484-0.99429.0317-0.5247-0.05130.7996-0.1257-0.2391-0.9747-1.12330.15180.85291.1194-0.0176-0.12010.88770.07011.5993-41.956751.356654.5132
810.5222.86044.37197.742-1.62069.8382-0.11391.0160.4401-1.308-0.0024-0.68450.2845-0.05130.1551.41760.13890.09960.94780.08440.9949-46.283242.806637.5682
93.28451.6272-1.01554.9559-1.90444.9176-0.28590.0384-0.2177-0.54140.091-0.78430.18670.23540.24740.86160.2392-0.0020.6261-0.06430.8665-48.994227.782859.5251
1010.13861.64042.44779.35170.78026.12310.4719-0.9653-0.7990.0564-0.2020.10740.9744-0.6307-0.48321.1660.130.14880.79340.21520.9347-58.303714.56470.0237
118.44762.5672-0.87248.193-2.78377.0056-0.34651.1574-0.4528-1.6060.41190.672-0.2279-0.5478-0.14111.29320.0886-0.31741.1034-0.09050.9219-68.160323.83541.7961
125.02091.9668-1.57796.9785-2.79039.1301-0.3144-1.00350.97991.2611-0.070.2456-1.1477-0.41320.25991.00210.2629-0.17020.9805-0.2531.05-49.859243.547171.6352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 107 )
2X-RAY DIFFRACTION2chain 'A' and (resid 108 through 252 )
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 361 )
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 77 )
5X-RAY DIFFRACTION5chain 'B' and (resid 78 through 192 )
6X-RAY DIFFRACTION6chain 'B' and (resid 193 through 361 )
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 107 )
8X-RAY DIFFRACTION8chain 'C' and (resid 108 through 192 )
9X-RAY DIFFRACTION9chain 'C' and (resid 193 through 361 )
10X-RAY DIFFRACTION10chain 'D' and (resid 0 through 77 )
11X-RAY DIFFRACTION11chain 'D' and (resid 78 through 256 )
12X-RAY DIFFRACTION12chain 'D' and (resid 257 through 361 )

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