[English] 日本語
Yorodumi
- PDB-8dy1: Crystal Structure of scFv CAT2200 LH in complex with IL-17A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dy1
TitleCrystal Structure of scFv CAT2200 LH in complex with IL-17A
Components
  • Interleukin-17A
  • scFv CAT2200 LH
KeywordsIMMUNE SYSTEM / scFv / stapled scFv / spFv / germline scFv / single chain Fv / scFv stabilizations / antibody / antibody antigen complex
Function / homology
Function and homology information


positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / intestinal epithelial structure maintenance / negative regulation of inflammatory response to wounding / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / cell death / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / positive regulation of bicellular tight junction assembly / fibroblast activation / positive regulation of osteoclast differentiation / positive regulation of cytokine production involved in inflammatory response / keratinocyte proliferation / cellular response to interleukin-1 / defense response to fungus / keratinocyte differentiation / Notch signaling pathway / positive regulation of interleukin-12 production / positive regulation of interleukin-1 beta production / cytokine activity / response to wounding / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / cell-cell signaling / gene expression / Interleukin-4 and Interleukin-13 signaling / defense response to Gram-negative bacterium / adaptive immune response / defense response to Gram-positive bacterium / inflammatory response / immune response / protein heterodimerization activity / external side of plasma membrane / innate immune response / apoptotic process / 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: 2.68 Å
Model detailsCrystal Structure of spFv GLK1 in LH configuration
AuthorsLuo, J. / Armstrong, A.A.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Mabs / Year: 2023
Title: "Stapling" scFv for multispecific biotherapeutics of superior properties.
Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / ...Authors: Boucher, L.E. / Prinslow, E.G. / Feldkamp, M. / Yi, F. / Nanjunda, R. / Wu, S.J. / Liu, T. / Lacy, E.R. / Jacobs, S. / Kozlyuk, N. / Del Rosario, B. / Wu, B. / Aquino, P. / Davidson, R.C. / Heyne, S. / Mazzanti, N. / Testa, J. / Diem, M.D. / Gorre, E. / Mahan, A. / Nanda, H. / Gunawardena, H.P. / Gervais, A. / Armstrong, A.A. / Teplyakov, A. / Huang, C. / Zwolak, A. / Chowdhury, P. / Cheung, W.C. / Luo, J.
History
DepositionAug 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 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
A: Interleukin-17A
B: Interleukin-17A
C: scFv CAT2200 LH
D: scFv CAT2200 LH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,0368
Polymers81,6524
Non-polymers3844
Water1,31573
1
A: Interleukin-17A
C: scFv CAT2200 LH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0184
Polymers40,8262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1540 Å2
ΔGint-39 kcal/mol
Surface area16650 Å2
MethodPISA
2
B: Interleukin-17A
D: scFv CAT2200 LH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0184
Polymers40,8262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-38 kcal/mol
Surface area15940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.930, 62.050, 111.710
Angle α, β, γ (deg.)90.000, 99.690, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain C and (resid 2 through 110 or resid 131...
21(chain D and (resid 2 through 110 or resid 131...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11PHEPHELEULEU(chain C and (resid 2 through 110 or resid 131...CC2 - 1102 - 110
12GLUGLULEULEU(chain C and (resid 2 through 110 or resid 131...CC131 - 148131 - 148
13LEULEUVALVAL(chain C and (resid 2 through 110 or resid 131...CC150 - 194150 - 194
14GLYGLYSERSER(chain C and (resid 2 through 110 or resid 131...CC196 - 205196 - 205
15ASNASNSERSER(chain C and (resid 2 through 110 or resid 131...CC207 - 247207 - 247
21PHEPHELEULEU(chain D and (resid 2 through 110 or resid 131...DD2 - 1102 - 110
22GLUGLUGLYGLY(chain D and (resid 2 through 110 or resid 131...DD131 - 140131 - 140
23ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
24ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
25ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
26ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
27ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
28ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248
29ASNASNSERSER(chain D and (resid 2 through 110 or resid 131...DD1 - 2481 - 248

-
Components

#1: Protein Interleukin-17A / IL-17 / IL-17A / Cytotoxic T-lymphocyte-associated antigen 8 / CTLA-8


Mass: 14209.944 Da / Num. of mol.: 2 / Mutation: K93Q, C129S, A155Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL17A, CTLA8, IL17 / Plasmid: pUNDER / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: Q16552
#2: Antibody scFv CAT2200 LH


Mass: 26616.104 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pUNDER / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.5 / Details: 100 mM Tris, 200 mM LiSO4, 18% PEG 3350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 17, 2016 / Details: mirrors
RadiationMonochromator: ACCEL SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.68→43.69 Å / Num. obs: 18382 / % possible obs: 92.2 % / Observed criterion σ(I): -3 / Redundancy: 3.22 % / Biso Wilson estimate: 47.405 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.066 / Rrim(I) all: 0.08 / Χ2: 0.914 / Net I/σ(I): 13.09
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.68-2.750.5222.5713410.9230.6291.8
2.75-2.820.2834.0614140.9560.33599.2
2.82-2.910.2384.5813790.970.28198.7
2.91-30.1915.8713240.9780.22799
3-3.090.1846.1513090.9690.22299
3.09-3.20.1338.3312320.9830.15998.9
3.2-3.320.1099.3212030.9910.13198.7
3.32-3.460.09210.397310.9910.11360.6
3.46-3.610.0912.3810070.990.10991.4
3.61-3.790.07214.486870.9930.0964.2
3.79-40.06415.517600.9930.0872.1
4-4.240.0520.469510.9960.0698.3
4.24-4.530.04323.829030.9970.05298.2
4.53-4.890.0425.578270.9960.04898.2
4.89-5.360.0425.097860.9970.04898.5
5.36-5.990.04222.567070.9970.05198.9
5.99-6.920.04122.976320.9960.0598.8
6.92-8.470.03526.565360.9980.04198.5
8.47-11.990.02829.724190.9980.03498.1
11.99-43.690.02429.912340.9990.02995.1

-
Processing

Software
NameVersionClassification
PHENIX1.18_3855refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QHU

4qhu


Resolution: 2.68→43.69 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 29.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2682 854 4.66 %
Rwork0.2209 17489 -
obs0.2231 18343 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 92.64 Å2 / Biso mean: 48.0345 Å2 / Biso min: 20.66 Å2
Refinement stepCycle: final / Resolution: 2.68→43.69 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4850 0 20 73 4943
Biso mean--52.04 43.83 -
Num. residues----646
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11C1940X-RAY DIFFRACTION11.964TORSIONAL
12D1940X-RAY DIFFRACTION11.964TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.68-2.850.40551370.3063001313896
2.85-3.070.32351360.25893109324599
3.07-3.380.26841600.24593112327299
3.38-3.860.27261320.24872156228869
3.86-4.870.24021300.18162907303792
4.87-43.690.24181590.20083204336399

+
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