[English] 日本語
Yorodumi
- PDB-5mvz: Fab 4AB007 bound to Interleukin-1-beta -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5mvz
TitleFab 4AB007 bound to Interleukin-1-beta
Components
  • Fab 4AB007 H-chain
  • Fab 4AB007 L-chain
  • Interleukin-1 beta
KeywordsSIGNALING PROTEIN / Interleukin-1-beta / Fab 4AB007
Function / homology
Function and homology information


positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process ...positive regulation of T cell mediated immunity / positive regulation of cell adhesion molecule production / negative regulation of adiponectin secretion / monocyte aggregation / negative regulation of lipid metabolic process / smooth muscle adaptation / positive regulation of lipid catabolic process / negative regulation of D-glucose transmembrane transport / regulation of nitric-oxide synthase activity / hyaluronan biosynthetic process / positive regulation of T-helper 1 cell cytokine production / positive regulation of complement activation / cellular response to interleukin-17 / positive regulation of RNA biosynthetic process / positive regulation of tight junction disassembly / positive regulation of prostaglandin biosynthetic process / positive regulation of prostaglandin secretion / negative regulation of gap junction assembly / positive regulation of immature T cell proliferation in thymus / vascular endothelial growth factor production / positive regulation of fever generation / positive regulation of neuroinflammatory response / regulation of defense response to virus by host / positive regulation of platelet-derived growth factor receptor signaling pathway / fever generation / CLEC7A/inflammasome pathway / regulation of establishment of endothelial barrier / Interleukin-1 processing / response to carbohydrate / interleukin-1 receptor binding / positive regulation of heterotypic cell-cell adhesion / positive regulation of monocyte chemotactic protein-1 production / positive regulation of p38MAPK cascade / positive regulation of macrophage derived foam cell differentiation / negative regulation of synaptic transmission / positive regulation of granulocyte macrophage colony-stimulating factor production / positive regulation of membrane protein ectodomain proteolysis / positive regulation of vascular endothelial growth factor receptor signaling pathway / regulation of canonical NF-kappaB signal transduction / interleukin-1-mediated signaling pathway / response to ATP / Interleukin-10 signaling / positive regulation of vascular endothelial growth factor production / positive regulation of cell division / positive regulation of glial cell proliferation / Pyroptosis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of neurogenesis / ectopic germ cell programmed cell death / negative regulation of lipid catabolic process / positive regulation of epithelial to mesenchymal transition / regulation of ERK1 and ERK2 cascade / Purinergic signaling in leishmaniasis infection / negative regulation of MAPK cascade / JNK cascade / positive regulation of T cell proliferation / extrinsic apoptotic signaling pathway in absence of ligand / neutrophil chemotaxis / embryo implantation / positive regulation of interleukin-2 production / astrocyte activation / positive regulation of mitotic nuclear division / regulation of insulin secretion / negative regulation of insulin receptor signaling pathway / response to interleukin-1 / secretory granule / positive regulation of protein export from nucleus / cytokine activity / positive regulation of interleukin-8 production / positive regulation of JNK cascade / cellular response to mechanical stimulus / positive regulation of non-canonical NF-kappaB signal transduction / Interleukin-1 signaling / negative regulation of neurogenesis / positive regulation of interleukin-6 production / integrin binding / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / cytokine-mediated signaling pathway / positive regulation of inflammatory response / positive regulation of angiogenesis / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / lysosome / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of MAPK cascade / defense response to Gram-positive bacterium / immune response / positive regulation of cell migration / inflammatory response / protein domain specific binding / negative regulation of cell population proliferation / positive regulation of cell population proliferation / apoptotic process / positive regulation of gene expression
Similarity search - Function
Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) ...Interleukin-1 propeptide / Interleukin-1 propeptide / Interleukin-1 conserved site / Interleukin-1 signature. / Interleukin-1 homologues / Interleukin-1 family / Interleukin-1 / 18 / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Multifunctional fusion protein / Interleukin-1 beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.15 Å
AuthorsStark, W. / Seibert, V.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
KTI12972.1 Switzerland
CitationJournal: To Be Published
Title: Structure of a novel, fully Human Fab binding to Interleukin 1-beta.
Authors: Stark, W. / Seibert, V.
History
DepositionJan 17, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 15, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Advisory / Data collection / Derived calculations
Category: pdbx_data_processing_status / pdbx_validate_symm_contact ...pdbx_data_processing_status / pdbx_validate_symm_contact / struct_conn / struct_conn_type
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Fab 4AB007 H-chain
L: Fab 4AB007 L-chain
U: Interleukin-1 beta
A: Fab 4AB007 H-chain
B: Fab 4AB007 L-chain
V: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)147,63614
Polymers146,8996
Non-polymers7378
Water11,422634
1
H: Fab 4AB007 H-chain
L: Fab 4AB007 L-chain
U: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8187
Polymers73,4503
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Fab 4AB007 H-chain
B: Fab 4AB007 L-chain
V: Interleukin-1 beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,8187
Polymers73,4503
Non-polymers3684
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.041, 158.385, 153.437
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11L-426-

HOH

21U-227-

HOH

31B-519-

HOH

41V-224-

HOH

51V-227-

HOH

-
Components

#1: Antibody Fab 4AB007 H-chain


Mass: 25437.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Fab 4AB007 L-chain


Mass: 27678.803 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: Protein Interleukin-1 beta


Mass: 20333.020 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B / Production host: Homo sapiens (human) / References: UniProt: B5BUQ8, UniProt: P01584*PLUS
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 634 / 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 Å3/Da / Density % sol: 68.86 % / Description: plates
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: Protein mix: 10mg/ml Protein 10mM Imidazole buffer, pH=8.0 50mM NaCl Reservoir: 18% PEG4000 (w/v), 0.1M Hepes pH=7.0, 10mM ATP, Drop Ratio 1:1

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1.000, 2.066
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
22.0661
ReflectionResolution: 2.093→47.68 Å / Num. obs: 79698 / % possible obs: 95.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.085 / Net I/σ(I): 10.4
Reflection shellResolution: 2.093→2.21 Å / % possible all: 94.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.15→47.68 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.897 / SU B: 7.628 / SU ML: 0.199 / Cross valid method: THROUGHOUT / ESU R: 0.264 / ESU R Free: 0.228 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28107 3665 5 %RANDOM
Rwork0.21945 ---
obs0.22253 69661 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 65.942 Å2
Baniso -1Baniso -2Baniso -3
1--0.59 Å2-0 Å20 Å2
2---0.94 Å2-0 Å2
3---1.53 Å2
Refinement stepCycle: 1 / Resolution: 2.15→47.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8857 0 48 634 9539
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.029105
X-RAY DIFFRACTIONr_bond_other_d0.0020.028455
X-RAY DIFFRACTIONr_angle_refined_deg1.6771.96112346
X-RAY DIFFRACTIONr_angle_other_deg0.862319587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.64951140
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.72724.751362
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.633151514
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.681532
X-RAY DIFFRACTIONr_chiral_restr0.0960.21385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02110208
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022000
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.0166.494593
X-RAY DIFFRACTIONr_mcbond_other5.016.494592
X-RAY DIFFRACTIONr_mcangle_it6.6269.7165722
X-RAY DIFFRACTIONr_mcangle_other6.6279.7175723
X-RAY DIFFRACTIONr_scbond_it4.8686.7744510
X-RAY DIFFRACTIONr_scbond_other4.8686.7744510
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.55610.026625
X-RAY DIFFRACTIONr_long_range_B_refined9.2753.0510565
X-RAY DIFFRACTIONr_long_range_B_other9.2753.0510565
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 268 -
Rwork0.288 5086 -
obs--99.42 %

+
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