[English] 日本語
Yorodumi
- PDB-8dy5: Crystal Structure of spFv CAT2200 LH in complex with IL-17A -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8dy5
TitleCrystal Structure of spFv CAT2200 LH in complex with IL-17A
Components
  • Interleukin-17A
  • spFv 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 / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway ...positive regulation of interleukin-16 production / granulocyte migration / positive regulation of antimicrobial peptide production / Interleukin-17 signaling / cell death / interleukin-17A-mediated signaling pathway / positive regulation of interleukin-23 production / negative regulation of inflammatory response to wounding / positive regulation of chemokine (C-X-C motif) ligand 1 production / interleukin-17-mediated signaling pathway / intestinal epithelial structure maintenance / fibroblast activation / positive regulation of bicellular tight junction assembly / 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 / positive regulation of interleukin-6 production / response to wounding / positive regulation of tumor necrosis factor production / cell-cell signaling / defense response to Gram-negative bacterium / Interleukin-4 and Interleukin-13 signaling / gene expression / adaptive immune response / defense response to Gram-positive bacterium / immune response / inflammatory 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
Model detailsCrystal Structure of spFv GLK1 in LH configuration
AuthorsLuo, J. / Boucher, L.E.
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
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: spFv CAT2200 LH
B: spFv CAT2200 LH
C: Interleukin-17A
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,5627
Polymers81,4624
Non-polymers1003
Water5,152286
1
A: spFv CAT2200 LH
C: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7673
Polymers40,7312
Non-polymers351
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: spFv CAT2200 LH
D: Interleukin-17A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7964
Polymers40,7312
Non-polymers642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.430, 226.380, 75.350
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11C-213-

HOH

21D-312-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 9 or resid 11...
21(chain B and (resid 1 through 9 or resid 11...

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
11ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 91 - 9
12SERSERASNASN(chain A and (resid 1 through 9 or resid 11...AA11 - 3111 - 31
13ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
14ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
15ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
16ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
17ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
18ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
19ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
110ASNASNSERSER(chain A and (resid 1 through 9 or resid 11...AA1 - 2441 - 244
21ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 91 - 9
22SERSERASNASN(chain B and (resid 1 through 9 or resid 11...BB11 - 3111 - 31
23TYRTYRTYRTYR(chain B and (resid 1 through 9 or resid 11...BB3232
24ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
25ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
26ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
27ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
28ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
29ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244
210ASNASNSERSER(chain B and (resid 1 through 9 or resid 11...BB1 - 2441 - 244

-
Components

-
Antibody / Protein , 2 types, 4 molecules ABCD

#1: Antibody spFv CAT2200 LH


Mass: 26521.256 Da / Num. of mol.: 2 / Mutation: T28G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IL-17A / Plasmid: pUNDER / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: 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 (production host): Expi293 / Production host: Homo sapiens (human) / References: UniProt: Q16552

-
Non-polymers , 4 types, 289 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 286 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.16 Å3/Da / Density % sol: 42.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion / Details: 400 mM LiSO4, 15.5% 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: Jul 18, 2018 / 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: 2.2→45.26 Å / Num. obs: 36090 / % possible obs: 99.4 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 41.718 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.12 / Rrim(I) all: 0.134 / Χ2: 0.838 / Net I/σ(I): 10.27
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.261.0121.9826300.7241.12799.5
2.26-2.320.9782.0425870.7591.0999.8
2.32-2.390.8162.4125080.8080.9199.8
2.39-2.460.6712.9224290.8470.7599.7
2.46-2.540.5543.523840.8850.6299.8
2.54-2.630.4214.6622680.9280.4799.5
2.63-2.730.3545.422050.9480.39499.5
2.73-2.840.2836.621380.9570.31599.9
2.84-2.970.2138.2220490.9790.23899.9
2.97-3.110.179.9719550.9860.1999.7
3.11-3.280.12712.0218780.9910.14399.7
3.28-3.480.09315.4717520.9950.10499.3
3.48-3.720.07718.6716610.9960.08699.5
3.72-4.020.06620.6715540.9970.07399.4
4.02-4.40.05523.7914350.9970.06199.2
4.4-4.920.04625.6613030.9980.05298.9
4.92-5.680.04624.5811490.9980.05298.6
5.68-6.960.0522.849770.9980.05697.3
6.96-9.840.0427.067760.9990.04598.4
9.84-45.260.03230.334520.9990.03795

-
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: 2.2→45.25 Å / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 25.83 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1803 5 %
Rwork0.1879 34266 -
obs0.1902 36069 99.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.3 Å2 / Biso mean: 42.8986 Å2 / Biso min: 21.14 Å2
Refinement stepCycle: final / Resolution: 2.2→45.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5021 0 3 286 5310
Biso mean--61.94 42.84 -
Num. residues----691
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A16X-RAY DIFFRACTION41.058TORSIONAL
12B16X-RAY DIFFRACTION41.058TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.260.30931360.25772599273599
2.26-2.330.35641390.256426372776100
2.33-2.40.33961350.247225702705100
2.4-2.490.28411380.238226222760100
2.49-2.590.29041390.22226322771100
2.59-2.70.26761370.19812600273799
2.7-2.850.28311380.194326262764100
2.85-3.020.24671390.180226312770100
3.03-3.260.22611380.186626332771100
3.26-3.590.2221400.16172656279699
3.59-4.10.17881390.16512638277799
4.1-5.170.18071400.15482671281199
5.17-45.250.23931450.20582751289698

+
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