[English] 日本語
Yorodumi
- PDB-7n0a: Structure of Human Leukaemia Inhibitory Factor with Fab MSC1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7n0a
TitleStructure of Human Leukaemia Inhibitory Factor with Fab MSC1
Components
  • Leukemia inhibitory factor
  • MSC-1 Fab Heavy chain
  • MSC-1 Fab Light chain
KeywordsCYTOKINE/IMMUNE SYSTEM / LIF / Cytokine / Antibody / Cancer therapeutics / CYTOKINE-IMMUNE SYSTEM complex
Function / homology
Function and homology information


leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / negative regulation of meiotic nuclear division / muscle organ morphogenesis / leukemia inhibitory factor signaling pathway / cell surface receptor signaling pathway via STAT / regulation of metanephric nephron tubule epithelial cell differentiation / positive regulation of peptidyl-serine phosphorylation of STAT protein ...leukemia inhibitory factor receptor binding / spongiotrophoblast differentiation / meiotic nuclear division / positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis / negative regulation of meiotic nuclear division / muscle organ morphogenesis / leukemia inhibitory factor signaling pathway / cell surface receptor signaling pathway via STAT / regulation of metanephric nephron tubule epithelial cell differentiation / positive regulation of peptidyl-serine phosphorylation of STAT protein / negative regulation of hormone secretion / trophoblast giant cell differentiation / lung vasculature development / lung lobe morphogenesis / positive regulation of macrophage differentiation / positive regulation of astrocyte differentiation / IL-6-type cytokine receptor ligand interactions / positive regulation of cell adhesion mediated by integrin / lung alveolus development / regulation of cell differentiation / Interleukin-10 signaling / somatic stem cell population maintenance / macrophage differentiation / decidualization / neuron development / blood vessel remodeling / positive regulation of tyrosine phosphorylation of STAT protein / embryo implantation / cytokine activity / stem cell differentiation / growth factor activity / cell morphogenesis / negative regulation of ERK1 and ERK2 cascade / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of fibroblast proliferation / positive regulation of peptidyl-serine phosphorylation / gene expression / fibroblast proliferation / Interleukin-4 and Interleukin-13 signaling / positive regulation of MAPK cascade / response to hypoxia / immune response / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of cell population proliferation / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / cytosol
Similarity search - Function
Leukemia inhibitory factor / Leukemia inhibitory factor /oncostatin / Leukemia inhibitory factor /oncostatin, conserved site / LIF / OSM family / LIF / OSM family signature. / leukemia inhibitory factor / Four-helical cytokine-like, core
Similarity search - Domain/homology
Leukemia inhibitory factor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsRaman, S. / Bosch, A. / Fransson, J. / Julien, J.P.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canada Research Chairs950231604 Canada
CitationJournal: Clin.Cancer Res. / Year: 2023
Title: Therapeutic Targeting of LIF Overcomes Macrophage-mediated Immunosuppression of the Local Tumor Microenvironment.
Authors: Hallett, R.M. / Bonfill-Teixidor, E. / Iurlaro, R. / Arias, A. / Raman, S. / Bayliss, P. / Egorova, O. / Neva-Alejo, A. / McGray, A.R. / Lau, E. / Bosch, A. / Beilschmidt, M. / Maetzel, D. / ...Authors: Hallett, R.M. / Bonfill-Teixidor, E. / Iurlaro, R. / Arias, A. / Raman, S. / Bayliss, P. / Egorova, O. / Neva-Alejo, A. / McGray, A.R. / Lau, E. / Bosch, A. / Beilschmidt, M. / Maetzel, D. / Fransson, J. / Huber-Ruano, I. / Anido, J. / Julien, J.P. / Giblin, P. / Seoane, J.
History
DepositionMay 25, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Feb 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name
Revision 1.3Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: Leukemia inhibitory factor
A: MSC-1 Fab Light chain
B: MSC-1 Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,3188
Polymers67,9763
Non-polymers1,3425
Water1267
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7050 Å2
ΔGint-12 kcal/mol
Surface area27990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.572, 109.380, 115.691
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

-
Components

-
Protein , 1 types, 1 molecules C

#1: Protein Leukemia inhibitory factor / LIF / Differentiation-stimulating factor / D factor / Melanoma-derived LPL inhibitor / MLPLI


Mass: 19796.904 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LIF, HILDA / Production host: Homo sapiens (human) / References: UniProt: P15018

-
Antibody , 2 types, 2 molecules AB

#2: Antibody MSC-1 Fab Light chain


Mass: 24033.744 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody MSC-1 Fab Heavy chain


Mass: 24145.084 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 2 types, 4 molecules

#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 2 types, 8 molecules

#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 7 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.82 Å3/Da / Density % sol: 56.37 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 19% (v/v) isopropanol, 19% (w/v) PEG 4000, 5% (v/v) glycerol, 0.095 M sodium citrate, pH 5.6

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332013463416 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332013463416 Å / Relative weight: 1
ReflectionResolution: 3.1→39.74 Å / Num. obs: 14528 / % possible obs: 98.4 % / Redundancy: 12 % / Biso Wilson estimate: 58.49 Å2 / CC1/2: 0.975 / Net I/σ(I): 5.1
Reflection shellResolution: 3.1→3.21 Å / Num. unique obs: 1427 / CC1/2: 0.597

-
Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XPREPdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PVH

1pvh


Resolution: 3.1→39.74 Å / SU ML: 0.4437 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.629
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.284 730 5.03 %
Rwork0.2318 13783 -
obs0.2345 14513 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.17 Å2
Refinement stepCycle: LAST / Resolution: 3.1→39.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4728 0 20 7 4755
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0024854
X-RAY DIFFRACTIONf_angle_d0.53386599
X-RAY DIFFRACTIONf_chiral_restr0.0383762
X-RAY DIFFRACTIONf_plane_restr0.0042841
X-RAY DIFFRACTIONf_dihedral_angle_d15.26882907
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.340.33571390.29872706X-RAY DIFFRACTION99.93
3.34-3.680.33191490.26912687X-RAY DIFFRACTION99.82
3.68-4.210.32091410.24522730X-RAY DIFFRACTION99.83
4.21-5.30.25681460.20422762X-RAY DIFFRACTION99.86
5.3-39.740.23961550.20322898X-RAY DIFFRACTION99.93

+
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://pdbjlvh1.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