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- PDB-6xm2: The structure of the 4A11.v7 antibody in complex with human TGFb2 -

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Basic information

Entry
Database: PDB / ID: 6xm2
TitleThe structure of the 4A11.v7 antibody in complex with human TGFb2
Components
  • 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
  • 4A11.v7 kappa light chain Fab (VL-CL) humanized
  • Transforming growth factor beta-2
KeywordsCYTOKINE/IMMUNE SYSTEM / TGFb antibody / CYTOKINE / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / ascending aorta morphogenesis / positive regulation of activation-induced cell death of T cells / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation ...regulation of timing of catagen / regulation of apoptotic process involved in outflow tract morphogenesis / negative regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / substantia propria of cornea development / ascending aorta morphogenesis / positive regulation of activation-induced cell death of T cells / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis / regulation of transforming growth factor beta2 production / atrial septum morphogenesis / pharyngeal arch artery morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / positive regulation of heart contraction / activation-induced cell death of T cells / glial cell migration / positive regulation of extracellular matrix disassembly / secondary palate development / negative regulation of macrophage cytokine production / somatic stem cell division / positive regulation of integrin biosynthetic process / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / heart valve morphogenesis / negative regulation of cartilage development / cardiac epithelial to mesenchymal transition / signaling / TGFBR3 regulates TGF-beta signaling / positive regulation of stress-activated MAPK cascade / neuron fate commitment / pericyte cell differentiation / transforming growth factor beta receptor binding / eye development / neural retina development / embryonic digestive tract development / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / cranial skeletal system development / ventricular trabecula myocardium morphogenesis / negative regulation of Ras protein signal transduction / embryo development ending in birth or egg hatching / outflow tract septum morphogenesis / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell-cell junction organization / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / atrioventricular valve morphogenesis / face morphogenesis / odontogenesis / endocardial cushion morphogenesis / Molecules associated with elastic fibres / hair follicle morphogenesis / cartilage condensation / dopamine biosynthetic process / generation of neurons / ventricular septum morphogenesis / positive regulation of Notch signaling pathway / uterus development / inner ear development / TGF-beta receptor signaling activates SMADs / hemopoiesis / positive regulation of cell division / positive regulation of SMAD protein signal transduction / positive regulation of epithelial cell migration / epithelial to mesenchymal transition / blood vessel remodeling / hair follicle development / ECM proteoglycans / cardiac muscle cell proliferation / neuron development / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / heart morphogenesis / positive regulation of cell cycle / extrinsic apoptotic signaling pathway / neutrophil chemotaxis / extrinsic apoptotic signaling pathway in absence of ligand / epithelial cell differentiation / transforming growth factor beta receptor signaling pathway / axon guidance / response to progesterone / platelet alpha granule lumen / negative regulation of angiogenesis / cytokine activity / skeletal system development / positive regulation of protein secretion / neural tube closure / regulation of actin cytoskeleton organization / growth factor activity / kidney development / wound healing / negative regulation of cell growth / positive regulation of immune response / response to wounding / positive regulation of miRNA transcription
Similarity search - Function
Transforming growth factor beta-2 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-2 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Transforming growth factor beta-2 proprotein
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.91 Å
AuthorsLupardus, P.J. / Yin, J.P.
CitationJournal: Sci Transl Med / Year: 2021
Title: TGF beta 2 and TGF beta 3 isoforms drive fibrotic disease pathogenesis.
Authors: Sun, T. / Huang, Z. / Liang, W.C. / Yin, J. / Lin, W.Y. / Wu, J. / Vernes, J.M. / Lutman, J. / Caplazi, P. / Jeet, S. / Wong, T. / Wong, M. / DePianto, D.J. / Morshead, K.B. / Sun, K.H. / ...Authors: Sun, T. / Huang, Z. / Liang, W.C. / Yin, J. / Lin, W.Y. / Wu, J. / Vernes, J.M. / Lutman, J. / Caplazi, P. / Jeet, S. / Wong, T. / Wong, M. / DePianto, D.J. / Morshead, K.B. / Sun, K.H. / Modrusan, Z. / Vander Heiden, J.A. / Abbas, A.R. / Zhang, H. / Xu, M. / N'Diaye, E.N. / Roose-Girma, M. / Wolters, P.J. / Yadav, R. / Sukumaran, S. / Ghilardi, N. / Corpuz, R. / Emson, C. / Meng, Y.G. / Ramalingam, T.R. / Lupardus, P. / Brightbill, H.D. / Seshasayee, D. / Wu, Y. / Arron, J.R.
History
DepositionJun 29, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 7, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 4A11.v7 kappa light chain Fab (VL-CL) humanized
B: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
C: 4A11.v7 kappa light chain Fab (VL-CL) humanized
D: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
E: 4A11.v7 kappa light chain Fab (VL-CL) humanized
F: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
G: 4A11.v7 kappa light chain Fab (VL-CL) humanized
H: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
I: Transforming growth factor beta-2
J: Transforming growth factor beta-2
K: Transforming growth factor beta-2
L: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)243,11212
Polymers243,11212
Non-polymers00
Water12,755708
1
A: 4A11.v7 kappa light chain Fab (VL-CL) humanized
B: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
G: 4A11.v7 kappa light chain Fab (VL-CL) humanized
H: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
K: Transforming growth factor beta-2
L: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)121,5566
Polymers121,5566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: 4A11.v7 kappa light chain Fab (VL-CL) humanized
D: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
E: 4A11.v7 kappa light chain Fab (VL-CL) humanized
F: 4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized
I: Transforming growth factor beta-2
J: Transforming growth factor beta-2


Theoretical massNumber of molelcules
Total (without water)121,5566
Polymers121,5566
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.415, 85.108, 112.732
Angle α, β, γ (deg.)99.150, 99.510, 97.320
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody
4A11.v7 kappa light chain Fab (VL-CL) humanized


Mass: 23673.074 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#2: Antibody
4A11.v7 heavy chain Fab (VH-CH1) IgG1 humanized


Mass: 24372.275 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Protein
Transforming growth factor beta-2 / Cetermin / Glioblastoma-derived T-cell suppressor factor / G-TSF


Mass: 12732.597 Da / Num. of mol.: 4 / Fragment: mature domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB2 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P61812
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 708 / Source method: isolated from a natural source / Formula: H2O
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: 2.44 Å3/Da / Density % sol: 49.68 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 1000, 0.1 M Tris pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.91→82.97 Å / Num. obs: 161613 / % possible obs: 90.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 31.75 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.073 / Net I/σ(I): 8.5
Reflection shellResolution: 1.91→2.01 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.494 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 8036 / CC1/2: 0.877 / % possible all: 88.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTERrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4KXZ

4kxz


Resolution: 1.91→82.97 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.244 --RANDOM
Rwork0.205 ---
obs-161613 90.5 %-
Displacement parametersBiso max: 123.06 Å2 / Biso mean: 41.6117 Å2 / Biso min: 17.9 Å2
Refinement stepCycle: LAST / Resolution: 1.91→82.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16409 0 0 708 17117

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