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- PDB-8ruu: Fabs derived from bimekizumab in complex with IL-17F -

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Basic information

Entry
Database: PDB / ID: 8ruu
TitleFabs derived from bimekizumab in complex with IL-17F
Components
  • Immunoblobulin heavy chain
  • Immunoblobulin light chain
  • Interleukin-17F
KeywordsIMMUNOSUPPRESSANT / Complex Fab bimekizumab IL-17F / IL-17A / BKZ / IMMUNE SYSTEM
Function / homology
Function and homology information


regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / cytokine receptor binding ...regulation of granulocyte macrophage colony-stimulating factor production / regulation of interleukin-2 production / positive regulation of lymphotoxin A production / regulation of interleukin-8 production / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / regulation of transforming growth factor beta receptor signaling pathway / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / cytokine receptor binding / positive regulation of cytokine production involved in inflammatory response / cartilage development / regulation of interleukin-6 production / cytokine binding / negative regulation of angiogenesis / positive regulation of cytokine production / cytokine activity / positive regulation of interleukin-6 production / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / protein heterodimerization activity / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region
Similarity search - Function
Interleukin-17, chordata / Interleukin-17 family / Interleukin-17 / Cystine-knot cytokine
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.81 Å
AuthorsAdams, R. / Lawson, A.D.G.
Funding support1items
OrganizationGrant numberCountry
Not funded
Citation
Journal: J Invest Dermatol. / Year: 2024
Title: Crystal Structure of Bimekizumab Fab Fragment in Complex with IL-17F Provides Molecular Basis for Dual IL-17A and IL-17F Inhibition.
Authors: Adams, R. / Bunick, C.G. / Lawson, A.D.G. / Gomez, B. / Shaw, S.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Towards automated crystallographic structure refinement with phenix.refine.
Authors: Afonine, P.V. / Grosse-Kunstleve, R.W. / Echols, N. / Headd, J.J. / Moriarty, N.W. / Mustyakimov, M. / Terwilliger, T.C. / Urzhumtsev, A. / Zwart, P.H. / Adams, P.D.
#2: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJan 31, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2024Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.3Nov 6, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Immunoblobulin heavy chain
C: Immunoblobulin light chain
X: Interleukin-17F
H: Immunoblobulin heavy chain
L: Immunoblobulin light chain
Y: Interleukin-17F
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,2768
Polymers126,1606
Non-polymers1,1162
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18020 Å2
ΔGint-77 kcal/mol
Surface area46090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.150, 141.750, 145.560
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Antibody Immunoblobulin heavy chain


Mass: 24522.445 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody Immunoblobulin light chain


Mass: 23635.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Protein Interleukin-17F / IL-17F / Cytokine ML-1


Mass: 14922.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17F / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q96PD4
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 894.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-3-4/a4-b1_a6-e1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}[(6+1)][b-L-Fucp]{}}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.: 1 / 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
Has ligand of interestN
Has protein modificationY

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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: 3.95 Å3/Da / Density % sol: 68.9 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / Details: PEG 8000, lithium sulphate, glycerol

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 28, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 2.81→81.95 Å / Num. obs: 50718 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 79.78 Å2 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.022 / Rrim(I) all: 0.056 / Net I/σ(I): 23.2
Reflection shellResolution: 2.81→2.88 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 2.9 / Num. unique obs: 25323 / Rpim(I) all: 0.258 / Rrim(I) all: 0.68 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
PHASERphasing
xia2data scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JPY

1jpy


Resolution: 2.81→81.95 Å / SU ML: 0.3981 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.1497
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2415 2442 4.82 %
Rwork0.2043 48201 -
obs0.206 50643 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 85.5 Å2
Refinement stepCycle: LAST / Resolution: 2.81→81.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8231 0 74 0 8305
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00718510
X-RAY DIFFRACTIONf_angle_d1.01911583
X-RAY DIFFRACTIONf_chiral_restr0.05631325
X-RAY DIFFRACTIONf_plane_restr0.00591477
X-RAY DIFFRACTIONf_dihedral_angle_d14.74053091
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.81-2.870.40271350.32382795X-RAY DIFFRACTION99.93
2.87-2.930.35211490.31012819X-RAY DIFFRACTION99.93
2.93-30.33491310.28332793X-RAY DIFFRACTION99.97
3-3.070.30981370.2782791X-RAY DIFFRACTION99.86
3.07-3.160.31031510.27772811X-RAY DIFFRACTION99.97
3.16-3.250.30251360.27122789X-RAY DIFFRACTION99.86
3.25-3.350.33771560.27572801X-RAY DIFFRACTION100
3.35-3.470.2961420.24552816X-RAY DIFFRACTION100
3.47-3.610.2731540.22082800X-RAY DIFFRACTION99.86
3.61-3.780.24831430.21992804X-RAY DIFFRACTION99.97
3.78-3.980.25121240.20272863X-RAY DIFFRACTION99.9
3.98-4.230.20831460.18382832X-RAY DIFFRACTION99.93
4.23-4.550.18971500.15862832X-RAY DIFFRACTION99.9
4.55-5.010.19861610.1512841X-RAY DIFFRACTION99.87
5.01-5.730.20981510.16212852X-RAY DIFFRACTION99.9
5.73-7.220.23231500.19632912X-RAY DIFFRACTION99.97
7.23-81.950.22181260.20633050X-RAY DIFFRACTION99.37

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