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- PDB-13fj: TGFB1 IN COMPLEX WITH NIS793 FAB -

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Basic information

Entry
Database: PDB / ID: 13fj
TitleTGFB1 IN COMPLEX WITH NIS793 FAB
Components
  • NIS793 Fab heavy chain
  • NIS793 Fab light chain
  • Transforming growth factor beta-1
KeywordsCYTOKINE / TGFB1 / NIS793
Function / homology
Function and homology information


columnar/cuboidal epithelial cell maturation / branch elongation involved in mammary gland duct branching / 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 / positive regulation of primary miRNA processing / negative regulation of skeletal muscle tissue development / response to laminar fluid shear stress ...columnar/cuboidal epithelial cell maturation / branch elongation involved in mammary gland duct branching / 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 / positive regulation of primary miRNA processing / negative regulation of skeletal muscle tissue development / response to laminar fluid shear stress / regulation of enamel mineralization / embryonic liver development / regulation of cartilage development / macrophage derived foam cell differentiation / regulation of branching involved in mammary gland duct morphogenesis / TGFBR2 MSI Frameshift Mutants in Cancer / regulation of striated muscle tissue development / regulation of protein import into nucleus / regulation of blood vessel remodeling / tolerance induction to self antigen / cellular response to acetaldehyde / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / extracellular matrix assembly / negative regulation of hyaluronan biosynthetic process / type III transforming growth factor beta receptor binding / myofibroblast differentiation / positive regulation of odontogenesis / Langerhans cell differentiation / connective tissue replacement involved in inflammatory response wound healing / 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 / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / odontoblast differentiation / positive regulation of mesenchymal stem cell proliferation / positive regulation of receptor signaling pathway via STAT / positive regulation of isotype switching to IgA isotypes / membrane protein intracellular domain proteolysis / bronchiole development / retina vasculature development in camera-type eye / positive regulation of extracellular matrix assembly / mammary gland branching involved in thelarche / heart valve morphogenesis / lens fiber cell differentiation / TGFBR3 regulates TGF-beta signaling / positive regulation of vasculature development / hyaluronan catabolic process / ATP biosynthetic process / negative regulation of extracellular matrix disassembly / type II transforming growth factor beta receptor binding / positive regulation of branching involved in ureteric bud morphogenesis / receptor catabolic process / positive regulation of cardiac muscle cell differentiation / TGFBR1 LBD Mutants in Cancer / primordial germ cell migration / regulatory T cell differentiation / response to salt / endoderm development / negative regulation of cell-cell adhesion mediated by cadherin / negative regulation of myoblast differentiation / phospholipid homeostasis / positive regulation of mononuclear cell migration / negative regulation of biomineral tissue development / type I transforming growth factor beta receptor binding / positive regulation of chemotaxis / positive regulation of vascular permeability / negative regulation of interleukin-17 production / phosphate-containing compound metabolic process / response to cholesterol / cell-cell junction organization / oligodendrocyte development / surfactant homeostasis / sprouting angiogenesis / positive regulation of chemokine (C-X-C motif) ligand 2 production / negative regulation of ossification / aortic valve morphogenesis / RUNX3 regulates CDKN1A transcription / response to vitamin D / digestive tract development / face morphogenesis / neural tube development / positive regulation of fibroblast migration / ureteric bud development / negative regulation of release of sequestered calcium ion into cytosol / positive regulation of regulatory T cell differentiation / Molecules associated with elastic fibres / negative regulation of neuroblast proliferation / lung alveolus development / muscle cell cellular homeostasis / Syndecan interactions / cellular response to insulin-like growth factor stimulus / ventricular cardiac muscle tissue morphogenesis / negative regulation of phagocytosis / negative regulation of fat cell differentiation / odontogenesis of dentin-containing tooth / response to immobilization stress / positive regulation of interleukin-17 production / inner ear development
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 / Transforming growth factor-beta, C-terminal / Transforming growth factor beta like domain ...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
Similarity search - Domain/homology
Transforming growth factor beta-1 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsZhou, Z. / Zhu, X. / Clark, K.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: To Be Published
Title: TGFB1 IN COMPLEX WITH NIS793 FAB
Authors: Zhou, Z. / Zhu, X. / Clark, K.
History
DepositionMay 4, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 17, 2026Provider: repository / Type: Initial release

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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
H: NIS793 Fab heavy chain
I: NIS793 Fab heavy chain
L: NIS793 Fab light chain
M: NIS793 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,99311
Polymers118,5136
Non-polymers4805
Water1,71195
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15130 Å2
ΔGint-156 kcal/mol
Surface area46600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.705, 100.957, 138.911
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 12809.812 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB1, TGFB / Production host: Homo sapiens (human) / References: UniProt: P01137
#2: Antibody NIS793 Fab heavy chain


Mass: 23586.541 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody NIS793 Fab light chain


Mass: 22860.217 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 95 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.92 Å3/Da / Density % sol: 57.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.05M (NH4)2SO4, 0.05M BIS-TRIS 6.5 PH, 30% V/V PENTAERYTHRITOL PROPOXYLATE

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→100.96 Å / Num. obs: 36656 / % possible obs: 99.6 % / Redundancy: 12.9 % / Biso Wilson estimate: 86.13 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.148 / Rpim(I) all: 0.043 / Rrim(I) all: 0.154 / Χ2: 1.01 / Net I/σ(I): 11.5 / Num. measured all: 471252
Reflection shellResolution: 2.75→2.87 Å / % possible obs: 96.9 % / Redundancy: 9.5 % / Rmerge(I) obs: 1.766 / Mean I/σ(I) obs: 1.2 / Num. measured all: 40396 / Num. unique obs: 4267 / CC1/2: 0.663 / Rpim(I) all: 0.597 / Rrim(I) all: 1.868 / Χ2: 0.98 / Net I/σ(I) obs: 1.2 / % possible all: 96.9

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (16-JUL-2021)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→81.67 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.893 / SU R Cruickshank DPI: 0.955 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.946 / SU Rfree Blow DPI: 0.328 / SU Rfree Cruickshank DPI: 0.333
RfactorNum. reflection% reflectionSelection details
Rfree0.2543 1735 4.74 %RANDOM
Rwork0.2172 ---
obs0.2189 36596 99.5 %-
Displacement parametersBiso mean: 89.1 Å2
Baniso -1Baniso -2Baniso -3
1--18.5452 Å20 Å20 Å2
2---6.9745 Å20 Å2
3---25.5197 Å2
Refine analyzeLuzzati coordinate error obs: 0.4 Å
Refinement stepCycle: LAST / Resolution: 2.75→81.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8216 0 25 95 8336
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098460HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711561HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2735SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1396HARMONIC5
X-RAY DIFFRACTIONt_it8460HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.21
X-RAY DIFFRACTIONt_other_torsion20.55
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1125SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5852SEMIHARMONIC4
LS refinement shellResolution: 2.75→2.77 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.417 -5.33 %
Rwork0.3691 693 -
all0.372 732 -
obs--92.78 %
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)
11.4365-1.01311.37750.6285-0.52083.425-0.1882-0.1478-0.16990.2390.20070.0471-0.8062-0.1265-0.01250.18990.0192-0.0365-0.0928-0.0469-0.1079-3.2722-13.653218.1498
20.6552-0.98120.57011.612-0.8762.44560.10580.2753-0.109-0.179-0.00150.0533-0.11710.589-0.10430.0196-0.0648-0.0260.0642-0.0794-0.067611.1745-28.6416.6931
31.69880.72510.60222.37461.34151.87260.10170.3073-0.1363-0.0089-0.15010.0763-0.32090.11590.04840.07980.1108-0.01970.030.013-0.2181-7.2663-17.9462-12.9031
42.12871.2679-0.56011.9531-0.13621.56540.05430.0241-0.09360.36730.06370.0883-0.08160.1375-0.1180.07710.0973-0.029-0.0433-0.049-0.11336.2691-33.120147.7132
55.9221-1.628-3.16563.0773-0.40354.35940.0952-0.18470.2152-0.03560.01690.002-0.17320.4753-0.1121-0.08670.06540.0661-0.0369-0.056-0.222413.6388-36.4314-33.1869
61.8052-0.7308-1.33323.4910.46082.86580.2752-0.30450.2592-0.3490.2855-0.5424-0.44520.2161-0.5607-0.0163-0.13070.304-0.0728-0.22780.0053-7.7714-19.113479.4532
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|279 - A|390 }
2X-RAY DIFFRACTION2{ B|279 - B|390 }
3X-RAY DIFFRACTION3{ H|1 - H|121 L|1 - L|109 }
4X-RAY DIFFRACTION4{ I|1 - I|121 M|1 - M|109 }
5X-RAY DIFFRACTION5{ H|122 - H|224 L|110 - L|213 }
6X-RAY DIFFRACTION6{ I|122 - I|222 M|110 - M|211 }

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