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- PDB-4kv5: scFv GC1009 in complex with TGF-beta1. -

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Basic information

Entry
Database: PDB / ID: 4kv5
TitlescFv GC1009 in complex with TGF-beta1.
Components
  • Single-chain variable fragment GC1009
  • Transforming growth factor beta-1 proprotein
KeywordsIMMUNE SYSTEM / Cysteine knot / Fab / TGF-beta receptor mimetic / TGF-beta / TGF-beta receptor
Function / homology
Function and homology information


cellular response to acetaldehyde / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development ...cellular response to acetaldehyde / frontal suture morphogenesis / Influenza Virus Induced Apoptosis / adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains / positive regulation of microglia differentiation / regulation of interleukin-23 production / branch elongation involved in mammary gland duct branching / positive regulation of primary miRNA processing / columnar/cuboidal epithelial cell maturation / negative regulation of skeletal muscle tissue development / embryonic liver development / macrophage derived foam cell differentiation / response to laminar fluid shear stress / regulation of enamel mineralization / regulation of branching involved in mammary gland duct morphogenesis / regulation of cartilage development / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulation of blood vessel remodeling / regulation of protein import into nucleus / regulatory T cell differentiation / tolerance induction to self antigen / extracellular matrix assembly / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / myofibroblast differentiation / positive regulation of cardiac muscle cell differentiation / positive regulation of odontogenesis / connective tissue replacement involved in inflammatory response wound healing / Langerhans cell differentiation / TGFBR2 Kinase Domain Mutants in Cancer / positive regulation of smooth muscle cell differentiation / positive regulation of exit from mitosis / negative regulation of macrophage cytokine production / odontoblast differentiation / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of isotype switching to IgA isotypes / positive regulation of mesenchymal stem cell proliferation / positive regulation of receptor signaling pathway via STAT / membrane protein intracellular domain proteolysis / positive regulation of extracellular matrix assembly / retina vasculature development in camera-type eye / heart valve morphogenesis / bronchiole development / TGFBR3 regulates TGF-beta signaling / mammary gland branching involved in thelarche / hyaluronan catabolic process / positive regulation of vasculature development / lens fiber cell differentiation / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / receptor catabolic process / positive regulation of branching involved in ureteric bud morphogenesis / positive regulation of chemotaxis / TGFBR1 LBD Mutants in Cancer / type I transforming growth factor beta receptor binding / positive regulation of mononuclear cell migration / response to salt / germ cell migration / endoderm development / negative regulation of biomineral tissue development / phospholipid homeostasis / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / positive regulation of vascular permeability / response to cholesterol / oligodendrocyte development / cell-cell junction organization / negative regulation of interleukin-17 production / phosphate-containing compound metabolic process / surfactant homeostasis / deubiquitinase activator activity / sprouting angiogenesis / negative regulation of release of sequestered calcium ion into cytosol / negative regulation of ossification / positive regulation of chemokine (C-X-C motif) ligand 2 production / digestive tract development / aortic valve morphogenesis / RUNX3 regulates CDKN1A transcription / response to vitamin D / face morphogenesis / positive regulation of fibroblast migration / ureteric bud development / neural tube development / positive regulation of regulatory T cell differentiation / positive regulation of peptidyl-tyrosine phosphorylation / Molecules associated with elastic fibres / negative regulation of phagocytosis / positive regulation of epidermal growth factor receptor signaling pathway / negative regulation of neuroblast proliferation / lung alveolus development / Syndecan interactions / ventricular cardiac muscle tissue morphogenesis / muscle cell cellular homeostasis / cellular response to insulin-like growth factor stimulus / negative regulation of fat cell differentiation / odontogenesis of dentin-containing tooth
Similarity search - Function
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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines ...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 / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain / TGF-beta family profile. / Cystine-knot cytokine / Ribbon / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3 Å
AuthorsWei, R. / Moulin, A.G. / Mathieu, M.
CitationJournal: Protein Sci. / Year: 2014
Title: Structures of a pan-specific antagonist antibody complexed to different isoforms of TGF beta reveal structural plasticity of antibody-antigen interactions.
Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / ...Authors: Moulin, A. / Mathieu, M. / Lawrence, C. / Bigelow, R. / Levine, M. / Hamel, C. / Marquette, J.P. / Le Parc, J. / Loux, C. / Ferrari, P. / Capdevila, C. / Dumas, J. / Dumas, B. / Rak, A. / Bird, J. / Qiu, H. / Pan, C.Q. / Edmunds, T. / Wei, R.R.
History
DepositionMay 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 3, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_sheet_range
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 / _atom_site.label_seq_id / _entity_poly_seq.entity_id / _entity_poly_seq.num / _pdbx_poly_seq_scheme.asym_id / _pdbx_poly_seq_scheme.entity_id / _pdbx_poly_seq_scheme.ndb_seq_num / _pdbx_poly_seq_scheme.pdb_seq_num / _pdbx_poly_seq_scheme.pdb_strand_id / _pdbx_poly_seq_scheme.seq_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_unobs_or_zero_occ_residues.auth_asym_id / _pdbx_unobs_or_zero_occ_residues.auth_seq_id / _pdbx_unobs_or_zero_occ_residues.label_asym_id / _pdbx_unobs_or_zero_occ_residues.label_seq_id / _pdbx_validate_torsion.auth_asym_id / _pdbx_validate_torsion.auth_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_auth_seq_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.auth_asym_id / _struct_mon_prot_cis.auth_seq_id / _struct_mon_prot_cis.label_asym_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_auth_asym_id_2 / _struct_mon_prot_cis.pdbx_auth_seq_id_2 / _struct_mon_prot_cis.pdbx_label_asym_id_2 / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_auth_seq_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id
Revision 2.1Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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
C: Transforming growth factor beta-1 proprotein
D: Transforming growth factor beta-1 proprotein
A: Transforming growth factor beta-1 proprotein
B: Transforming growth factor beta-1 proprotein
J: Single-chain variable fragment GC1009
H: Single-chain variable fragment GC1009
E: Single-chain variable fragment GC1009
G: Single-chain variable fragment GC1009


Theoretical massNumber of molelcules
Total (without water)157,8668
Polymers157,8668
Non-polymers00
Water00
1
C: Transforming growth factor beta-1 proprotein
D: Transforming growth factor beta-1 proprotein


Theoretical massNumber of molelcules
Total (without water)25,6202
Polymers25,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2580 Å2
ΔGint-26 kcal/mol
Surface area12240 Å2
MethodPISA
2
A: Transforming growth factor beta-1 proprotein
B: Transforming growth factor beta-1 proprotein


Theoretical massNumber of molelcules
Total (without water)25,6202
Polymers25,6202
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-27 kcal/mol
Surface area12170 Å2
MethodPISA
3
J: Single-chain variable fragment GC1009


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12 kcal/mol
Surface area10560 Å2
MethodPISA
4
H: Single-chain variable fragment GC1009


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1530 Å2
ΔGint-12 kcal/mol
Surface area10460 Å2
MethodPISA
5
E: Single-chain variable fragment GC1009


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1620 Å2
ΔGint-13 kcal/mol
Surface area10440 Å2
MethodPISA
6
G: Single-chain variable fragment GC1009


Theoretical massNumber of molelcules
Total (without water)26,6571
Polymers26,6571
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
ΔGint-12 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.188, 171.769, 109.876
Angle α, β, γ (deg.)90.00, 111.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Transforming growth factor beta-1 proprotein


Mass: 12809.812 Da / Num. of mol.: 4 / Fragment: unp residues 279-390
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Escherichia coli (E. coli) / References: UniProt: P01137
#2: Antibody
Single-chain variable fragment GC1009


Mass: 26656.588 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET25b / Production host: Escherichia coli (E. coli) / Strain (production host): Origami2 (DE3)
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: 3.01 Å3/Da / Density % sol: 59.15 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5
Details: 16% PEG 4K, 0.1 M citrate, 4% 2-propanol , pH 5.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→30.96 Å / Num. all: 36102 / Num. obs: 36020 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
3.05-3.163.380.4671.9199.8
3.16-3.293.390.3912.3199.7
3.29-3.433.390.3612.4199.7
3.43-3.623.390.2842.9199.7
3.62-3.843.40.2224.1199.6
3.84-4.143.380.1884.1199.6
4.14-4.553.280.1216.8199.8
4.55-5.213.270.0948.8199.5
5.21-6.553.290.099.6199.7
6.55-30.963.20.05914.1198.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3→30.96 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.5 / σ(F): 0 / Phase error: 34.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3003 1925 5.63 %
Rwork0.2288 --
obs0.2329 34186 91.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.0874 Å2
Refinement stepCycle: LAST / Resolution: 3→30.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10542 0 0 0 10542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01110820
X-RAY DIFFRACTIONf_angle_d1.38414675
X-RAY DIFFRACTIONf_dihedral_angle_d15.243916
X-RAY DIFFRACTIONf_chiral_restr0.061617
X-RAY DIFFRACTIONf_plane_restr0.0071876
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.07490.39131120.31942004X-RAY DIFFRACTION80
3.0749-3.1580.38111280.29352054X-RAY DIFFRACTION82
3.158-3.25080.37391270.28052159X-RAY DIFFRACTION86
3.2508-3.35570.34281320.28722216X-RAY DIFFRACTION89
3.3557-3.47550.37321330.2962230X-RAY DIFFRACTION89
3.4755-3.61440.36081420.28242346X-RAY DIFFRACTION92
3.6144-3.77870.31561440.24832394X-RAY DIFFRACTION96
3.7787-3.97750.36111380.26862337X-RAY DIFFRACTION93
3.9775-4.22620.35281410.26492351X-RAY DIFFRACTION93
4.2262-4.55160.28681440.20382402X-RAY DIFFRACTION96
4.5516-5.00810.27481430.19852396X-RAY DIFFRACTION95
5.0081-5.72910.24271450.19792439X-RAY DIFFRACTION97
5.7291-7.2040.33611490.2222476X-RAY DIFFRACTION97
7.204-31.71390.20451470.16672457X-RAY DIFFRACTION96

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