[English] 日本語
Yorodumi
- PDB-6xm2: The structure of the 4A11.v7 antibody in complex with human TGFb2 -

+
Open data


ID or keywords:

Loading...

-
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 / cardioblast differentiation / uterine wall breakdown / positive regulation of timing of catagen / positive regulation of cardioblast differentiation / cardiac right ventricle morphogenesis ...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 / 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 / positive regulation of heart contraction / type III transforming growth factor beta receptor binding / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / negative regulation of macrophage cytokine production / glial cell migration / secondary palate development / somatic stem cell division / positive regulation of integrin biosynthetic process / atrial septum primum morphogenesis / endocardial cushion fusion / membranous septum morphogenesis / heart valve morphogenesis / TGFBR3 regulates TGF-beta signaling / cardiac epithelial to mesenchymal transition / eye development / signaling / positive regulation of stress-activated MAPK cascade / embryonic digestive tract development / transforming growth factor beta receptor binding / cranial skeletal system development / neural retina development / type II transforming growth factor beta receptor binding / pulmonary valve morphogenesis / activation of protein kinase activity / outflow tract septum morphogenesis / ventricular trabecula myocardium morphogenesis / cell-cell junction organization / negative regulation of Ras protein signal transduction / collagen fibril organization / embryonic limb morphogenesis / positive regulation of cell adhesion mediated by integrin / embryo development ending in birth or egg hatching / atrioventricular valve morphogenesis / odontogenesis / endocardial cushion morphogenesis / cardiac muscle cell proliferation / Molecules associated with elastic fibres / dopamine biosynthetic process / hair follicle morphogenesis / 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 epithelial cell migration / positive regulation of SMAD protein signal transduction / hair follicle development / epithelial to mesenchymal transition / ECM proteoglycans / neuron development / salivary gland morphogenesis / positive regulation of epithelial to mesenchymal transition / heart morphogenesis / extrinsic apoptotic signaling pathway / positive regulation of cell cycle / epithelial cell differentiation / neutrophil chemotaxis / transforming growth factor beta receptor signaling pathway / negative regulation of angiogenesis / platelet alpha granule lumen / response to progesterone / cytokine activity / kidney development / skeletal system development / positive regulation of protein secretion / neural tube closure / growth factor activity / wound healing / negative regulation of cell growth / cell morphogenesis / positive regulation of immune response / positive regulation of miRNA transcription / response to wounding / male gonad development / negative regulation of epithelial cell proliferation / positive regulation of neuron apoptotic process / Platelet degranulation / cell migration / regulation of cell population proliferation / amyloid-beta binding / heart development / positive regulation of cell growth / : / response to hypoxia
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
Phasing

PhasingMethod: molecular replacement

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more