[English] 日本語
Yorodumi
- PDB-7z4t: AAL160 FAB IN COMPLEX WITH HUMAN INTERLEUKIN-1 BETA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7z4t
TitleAAL160 FAB IN COMPLEX WITH HUMAN INTERLEUKIN-1 BETA
Components
  • AAL160 Fab heavy-chain
  • AAL160 light-chain
  • Interleukin-1 beta
KeywordsIMMUNE SYSTEM / OTHER / MONOCLONAL ANTIBODY / IL-1B / IMMUNOGLOBULIN
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 / negative regulation of gap junction assembly / positive regulation of prostaglandin secretion / 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 / regulation of neurogenesis / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / 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 / neutrophil chemotaxis / extrinsic apoptotic signaling pathway in absence of ligand / embryo implantation / positive regulation of interleukin-2 production / astrocyte activation / regulation of insulin secretion / positive regulation of mitotic nuclear division / 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 / negative regulation of neurogenesis / positive regulation of interleukin-6 production / cellular response to xenobiotic stimulus / positive regulation of type II interferon production / integrin binding / Interleukin-1 signaling / cytokine-mediated signaling pathway / positive regulation of angiogenesis / positive regulation of inflammatory response / positive regulation of nitric oxide biosynthetic process / cell-cell signaling / cellular response to lipopolysaccharide / Interleukin-4 and Interleukin-13 signaling / response to lipopolysaccharide / positive regulation of ERK1 and ERK2 cascade / lysosome / 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 / Immunoglobulins / Immunoglobulin-like ...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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.3 Å
AuthorsRondeau, J.M. / Lehmann, S.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Commun Biol / Year: 2023
Title: "Redirecting an anti-IL-1 beta antibody to bind a new, unrelated and computationally predicted epitope on hIL-17A".
Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, ...Authors: Fischman, S. / Levin, I. / Rondeau, J.M. / Strajbl, M. / Lehmann, S. / Huber, T. / Nimrod, G. / Cebe, R. / Omer, D. / Kovarik, J. / Bernstein, S. / Sasson, Y. / Demishtein, A. / Shlamkovich, T. / Bluvshtein, O. / Grossman, N. / Barak-Fuchs, R. / Zhenin, M. / Fastman, Y. / Twito, S. / Vana, T. / Zur, N. / Ofran, Y.
History
DepositionMar 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.title / _citation.year
Revision 1.2Oct 11, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: AAL160 Fab heavy-chain
I: Interleukin-1 beta
L: AAL160 light-chain


Theoretical massNumber of molelcules
Total (without water)65,1243
Polymers65,1243
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5120 Å2
ΔGint-30 kcal/mol
Surface area26080 Å2
Unit cell
Length a, b, c (Å)185.795, 37.167, 97.069
Angle α, β, γ (deg.)90.000, 114.920, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein AAL160 Fab heavy-chain


Mass: 24228.166 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens x Mus musculus hybrid cell line (mammal)
#2: Protein Interleukin-1 beta / IL-1 beta / Catabolin


Mass: 17395.832 Da / Num. of mol.: 1 / Fragment: Fab light-chain
Source method: isolated from a genetically manipulated source
Details: Mature form / Source: (gene. exp.) Homo sapiens (human) / Gene: IL1B, IL1F2 / Plasmid: pET derived / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): T1 / References: UniProt: P01584
#3: Antibody AAL160 light-chain


Mass: 23500.119 Da / Num. of mol.: 1 / Fragment: Interleukin-1beta
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Homo sapiens x Mus musculus hybrid cell line (mammal)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.33 Å3/Da / Density % sol: 47.29 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1M TRIS pH 8.5, 2.0M ammonium sulfate

-
Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Jul 27, 1999 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 3.3→48 Å / Num. obs: 9427 / % possible obs: 97.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 67.08 Å2 / Rmerge(I) obs: 0.159 / Χ2: 0.933 / Net I/σ(I): 5.28 / Num. measured all: 38916
Reflection shellResolution: 3.3→3.42 Å / Rmerge(I) obs: 0.505 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 1032 / Χ2: 1.02 / % possible all: 86.1

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
HKL-20001.9.1data reduction
SCALEPACK1.6.1data scaling
AMoRE3.4phasing
BUSTER2.11.8 (20-OCT-2021)refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2I1B

2i1b


Resolution: 3.3→29.34 Å / Cor.coef. Fo:Fc: 0.868 / Cor.coef. Fo:Fc free: 0.822 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.605
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2689 969 10.47 %RANDOM
Rwork0.2376 ---
obs0.2409 9257 98.2 %-
Displacement parametersBiso max: 109.58 Å2 / Biso mean: 62.82 Å2 / Biso min: 31.81 Å2
Baniso -1Baniso -2Baniso -3
1-9.6814 Å20 Å25.7981 Å2
2--1.5167 Å20 Å2
3----11.1981 Å2
Refine analyzeLuzzati coordinate error obs: 0.47 Å
Refinement stepCycle: final / Resolution: 3.3→29.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 0 0 4456
Num. residues----576
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2647SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1387HARMONIC5
X-RAY DIFFRACTIONt_it4563HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion595SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5831SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d8926HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16104HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion4.05
X-RAY DIFFRACTIONt_other_torsion14.57
LS refinement shellResolution: 3.3→3.33 Å / Rfactor Rfree error: 0 / Total num. of bins used: 49
RfactorNum. reflection% reflection
Rfree0.283 23 11.92 %
Rwork0.3096 170 -
all0.3056 193 -
obs--89.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.12990.3335-0.00470.40710.21240.4285-0.06670.20340.2899-0.0805-0.09070.09210.03820.00910.15740.07150.0331-0.0627-0.22920.06720.07-42.4449-1.736176.3475
26.2589-0.0127-0.2245.2803-0.33735.0348-0.39520.38440.45-0.1690.2982-0.1467-0.25330.67860.0971-0.2614-0.2524-0.08610.12870.12-0.2528-1.70256.644159.5986
35.99670.284-0.44880.3883-0.010.8887-0.54951.01850.3142-0.27460.06420.2260.0443-0.04960.48520.0161-0.1471-0.1199-0.12160.0641-0.0792-50.5663-4.922160.2395
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|* }H1 - 218
2X-RAY DIFFRACTION2{ I|* }I3 - 153
3X-RAY DIFFRACTION3{ L|* }L1 - 212

+
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