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- PDB-3eo1: Structure of the Fab Fragment of GC-1008 in Complex with Transfor... -

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Basic information

Entry
Database: PDB / ID: 3eo1
TitleStructure of the Fab Fragment of GC-1008 in Complex with Transforming Growth Factor-Beta 3
Components
  • GC-1008 Fab Heavy Chain
  • GC-1008 Fab Light Chain
  • Transforming growth factor beta-3
KeywordsIMMUNE SYSTEM/CYTOKINE / Antibody-cytokine complex / Growth factor / FAB fragment / Cardiomyopathy / Cleavage on pair of basic residues / Glycoprotein / Mitogen / Polymorphism / Secreted / IMMUNE SYSTEM-CYTOKINE COMPLEX
Function / homology
Function and homology information


uterine wall breakdown / detection of hypoxia / frontal suture morphogenesis / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding ...uterine wall breakdown / detection of hypoxia / frontal suture morphogenesis / embryonic neurocranium morphogenesis / type III transforming growth factor beta receptor binding / positive regulation of tight junction disassembly / negative regulation of macrophage cytokine production / secondary palate development / response to laminar fluid shear stress / type II transforming growth factor beta receptor binding / type I transforming growth factor beta receptor binding / mammary gland development / cell-cell junction organization / transforming growth factor beta binding / digestive tract development / IgG immunoglobulin complex / face morphogenesis / odontogenesis / Molecules associated with elastic fibres / positive regulation of filopodium assembly / Classical antibody-mediated complement activation / Initial triggering of complement / lung alveolus development / TGF-beta receptor signaling activates SMADs / negative regulation of vascular associated smooth muscle cell proliferation / positive regulation of SMAD protein signal transduction / inner ear development / positive regulation of cell division / FCGR activation / ECM proteoglycans / positive regulation of collagen biosynthetic process / Role of phospholipids in phagocytosis / positive regulation of epithelial to mesenchymal transition / salivary gland morphogenesis / immunoglobulin complex, circulating / positive regulation of stress fiber assembly / immunoglobulin receptor binding / T-tubule / FCGR3A-mediated IL10 synthesis / transforming growth factor beta receptor signaling pathway / platelet alpha granule lumen / complement activation, classical pathway / cytokine activity / Regulation of Complement cascade / response to progesterone / female pregnancy / positive regulation of protein secretion / antigen binding / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / negative regulation of transforming growth factor beta receptor signaling pathway / growth factor activity / Regulation of actin dynamics for phagocytic cup formation / response to estrogen / Platelet degranulation / regulation of cell population proliferation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / collagen-containing extracellular matrix / adaptive immune response / in utero embryonic development / negative regulation of neuron apoptotic process / positive regulation of MAPK cascade / blood microparticle / response to hypoxia / positive regulation of apoptotic process / negative regulation of cell population proliferation / intracellular membrane-bounded organelle / neuronal cell body / positive regulation of cell population proliferation / protein-containing complex binding / positive regulation of DNA-templated transcription / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular exosome / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Transforming growth factor beta-3 / 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-3 / 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 Cytokines, subunit B / Cystine-knot cytokines / Cystine-knot cytokine / Ribbon / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin heavy constant gamma 4 / Transforming growth factor beta-3 proprotein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGruetter, C. / Gruetter, M.G.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2008
Title: A cytokine-neutralizing antibody as a structural mimetic of 2 receptor interactions
Authors: Wilkinson, T. / Turner, R. / Podichetty, S. / Finch, D. / McCourt, M. / Loning, S. / Jermutus, L.
History
DepositionSep 26, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 2, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: GC-1008 Fab Light Chain
B: GC-1008 Fab Heavy Chain
C: Transforming growth factor beta-3
D: GC-1008 Fab Light Chain
E: GC-1008 Fab Heavy Chain
F: Transforming growth factor beta-3
G: GC-1008 Fab Light Chain
H: GC-1008 Fab Heavy Chain
I: Transforming growth factor beta-3
J: GC-1008 Fab Light Chain
K: GC-1008 Fab Heavy Chain
L: Transforming growth factor beta-3


Theoretical massNumber of molelcules
Total (without water)239,99712
Polymers239,99712
Non-polymers00
Water00
1
A: GC-1008 Fab Light Chain
B: GC-1008 Fab Heavy Chain
C: Transforming growth factor beta-3
D: GC-1008 Fab Light Chain
E: GC-1008 Fab Heavy Chain
F: Transforming growth factor beta-3


Theoretical massNumber of molelcules
Total (without water)119,9986
Polymers119,9986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-105.9 kcal/mol
Surface area48790 Å2
MethodPISA
2
G: GC-1008 Fab Light Chain
H: GC-1008 Fab Heavy Chain
I: Transforming growth factor beta-3
J: GC-1008 Fab Light Chain
K: GC-1008 Fab Heavy Chain
L: Transforming growth factor beta-3


Theoretical massNumber of molelcules
Total (without water)119,9986
Polymers119,9986
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12770 Å2
ΔGint-106 kcal/mol
Surface area48790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)149.040, 149.130, 149.660
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: Antibody
GC-1008 Fab Light Chain


Mass: 23425.934 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / Strain (production host): NS0
#2: Antibody
GC-1008 Fab Heavy Chain


Mass: 23838.779 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse) / Strain (production host): NS0 / References: UniProt: P01861*PLUS
#3: Protein
Transforming growth factor beta-3 / TGF-beta-3


Mass: 12734.504 Da / Num. of mol.: 4 / Fragment: UNP residues 301-412, receptor binding fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TGFB3 / Production host: Escherichia coli (E. coli) / References: UniProt: P10600
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN (ANTIBODY) DOES NOT CURRENTLY EXIST.

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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: 3.47 Å3/Da / Density % sol: 64.5 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.8
Details: 23% tert.-butanol, 0.1M sodium citrate, 0.2M phenoxyacetic acid, pH6.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.070645 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 24, 2006 / Details: BENT MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.070645 Å / Relative weight: 1
ReflectionResolution: 3.1→35 Å / Num. obs: 60296 / % possible obs: 97.9 % / Redundancy: 5 % / Rmerge(I) obs: 0.092 / Rsym value: 0.077 / Net I/σ(I): 20.8
Reflection shellResolution: 3.1→3.3 Å / Redundancy: 5 % / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 3.8 / Num. unique all: 10322 / Rsym value: 0.522 / % possible all: 96.4

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Processing

Software
NameClassification
XDSdata scaling
PHASERphasing
CNSrefinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3EO0, 1TGJ

3eo0

1tgj


Resolution: 3.1→35 Å / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.279 724 RANDOM
Rwork0.255 --
obs0.255 60296 -
all-61154 -
Displacement parametersBiso mean: 80.7 Å2
Refinement stepCycle: LAST / Resolution: 3.1→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16556 0 0 0 16556
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.413
X-RAY DIFFRACTIONc_bond_d0.006

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