[English] 日本語
Yorodumi
- PDB-9mdz: anti-IL23R VHH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9mdz
Titleanti-IL23R VHH
Componentsanti-IL23R VHH
KeywordsIMMUNE SYSTEM / IBD / Inflammatory Bowel Disease / inflammation / immunology
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsKiefer, J.R. / Koerber, J.T. / Ota, N. / Davies, C. / Wallweber, H.A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2025
Title: Engineering a protease-stable, oral single-domain antibody to inhibit IL-23 signaling.
Authors: Ota, N. / Davies, C.W. / Kang, J. / Yan, D. / Scherl, A. / Wong, A. / Cook, R. / Tao, X. / Dunlap, D. / Klabunde, S. / Mantik, P. / Mohanan, V. / Lin, W. / McBride, J. / Sadekar, S. / ...Authors: Ota, N. / Davies, C.W. / Kang, J. / Yan, D. / Scherl, A. / Wong, A. / Cook, R. / Tao, X. / Dunlap, D. / Klabunde, S. / Mantik, P. / Mohanan, V. / Lin, W. / McBride, J. / Sadekar, S. / Storek, K.M. / Lupardus, P. / Ye, Z. / Ackerly Wallweber, H. / Kiefer, J.R. / Xu, M. / Chan, P. / Nagapudi, K. / Yi, T. / Koerber, J.T.
History
DepositionDec 5, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 21, 2025Provider: repository / Type: Initial release
Revision 1.1Jun 11, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
E: anti-IL23R VHH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3233
Polymers13,1381
Non-polymers1842
Water4,071226
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.615, 125.615, 41.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422
Components on special symmetry positions
IDModelComponents
11E-331-

HOH

21E-378-

HOH

31E-436-

HOH

41E-476-

HOH

51E-516-

HOH

-
Components

#1: Antibody anti-IL23R VHH


Mass: 13138.472 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Cell line (production host): CHO / Production host: Cricetulus griseus (Chinese hamster)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 226 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.12 Å3/Da / Density % sol: 60.57 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 7 / Details: 800 mM sodium succinate, pH 7

-
Data collection

DiffractionMean temperature: 103 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1.00005 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00005 Å / Relative weight: 1
ReflectionResolution: 1.27→44.41 Å / Num. obs: 42302 / % possible obs: 97.2 % / Redundancy: 10.8 % / CC1/2: 1 / Rmerge(I) obs: 0.037 / Rpim(I) all: 0.011 / Rrim(I) all: 0.038 / Χ2: 0.71 / Net I/σ(I): 29 / Num. measured all: 456156
Reflection shellResolution: 1.27→1.3 Å / % possible obs: 64.3 % / Redundancy: 2.3 % / Rmerge(I) obs: 0.332 / Num. measured all: 3080 / Num. unique obs: 1366 / CC1/2: 0.847 / Rpim(I) all: 0.246 / Rrim(I) all: 0.418 / Χ2: 0.28 / Net I/σ(I) obs: 1.4

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.27→39.72 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 14.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1593 2092 4.95 %
Rwork0.1446 --
obs0.1453 42297 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.27→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 0 12 226 1163
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_d0.883
X-RAY DIFFRACTIONf_dihedral_angle_d18.824367
X-RAY DIFFRACTIONf_chiral_restr0.076145
X-RAY DIFFRACTIONf_plane_restr0.023187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.30.32131000.27761887X-RAY DIFFRACTION69
1.3-1.340.1991380.19562458X-RAY DIFFRACTION91
1.34-1.370.22181300.17472664X-RAY DIFFRACTION98
1.37-1.410.16451350.16582716X-RAY DIFFRACTION100
1.41-1.460.19071440.17412722X-RAY DIFFRACTION100
1.46-1.510.19091550.16112712X-RAY DIFFRACTION100
1.51-1.570.18461430.14382752X-RAY DIFFRACTION100
1.57-1.640.16891480.13612722X-RAY DIFFRACTION100
1.64-1.730.14281470.14062732X-RAY DIFFRACTION100
1.73-1.840.13761510.14852728X-RAY DIFFRACTION100
1.84-1.980.15671380.13152783X-RAY DIFFRACTION100
1.98-2.180.14211460.1252756X-RAY DIFFRACTION100
2.18-2.50.14171320.13282790X-RAY DIFFRACTION100
2.5-3.140.15561520.1462811X-RAY DIFFRACTION100
3.14-39.720.161330.14512972X-RAY DIFFRACTION100
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)
10.51650.24880.10230.8360.10550.0267-0.0265-0.62080.00520.55030.03550.0676-0.0562-0.7597-0.01140.1810.0233-0.00270.20760.01250.1157-19.820835.61679.715
20.02450.04050.02340.2702-0.16620.7478-0.0620.06760.0773-0.16420.0430.1808-0.1393-0.28890.03650.1225-0.0119-0.03070.17490.0080.1119-24.634630.8317-13.5068
30.5257-0.179-0.41750.21610.13360.33160.0131-0.12140.1444-0.02630.0668-0.0007-0.0808-0.02690.00010.11980.0092-0.00660.1215-0.01450.1255-14.85340.345.3316
40.317-0.035-0.01040.1151-0.1340.22560.072-0.0592-0.02880.0784-0.0183-0.06120.06190.0145-00.0929-0.00320.00110.1120.00140.1029-12.204831.1120.2755
50.84460.02710.04430.0550.02320.46410.0917-0.0068-0.36680.1295-0.0562-0.24660.118-0.0248-0.00010.1197-0.0053-0.01870.11370.00710.1742-10.643925.4718-1.4388
60.8610.34320.00530.5266-0.43130.55350.02240.1560.1241-0.04020.0397-0.0527-0.0827-0.04320.00260.09570.00710.00430.1320.00610.123-8.098738.0152-5.4671
70.19390.1884-0.31150.215-0.30.48770.07440.03130.11320.05950.06760.0284-0.0804-0.10930.00090.11070.01160.00310.12530.00690.132-16.506441.7916-1.7118
80.9254-0.03950.37590.5099-0.17750.2353-0.03510.11910.0038-0.07150.0156-0.01030.04820.095200.1083-0.01340.0050.126-0.00020.101-15.703929.1883-5.3251
90.37970.06530.08230.3589-0.2080.53890.0411-0.3696-0.0490.0473-0.0979-0.12480.05970.1127-00.1187-0.0037-0.0060.18550.00860.1302-6.909331.93489.0142
100.2151-0.046-0.17080.38340.06320.3494-0.19630.15150.0014-0.30760.0620.1742-0.0967-0.2238-0.01110.1529-0.0387-0.02280.1595-0.0060.1083-24.531825.6394-10.2465
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'E' and (resid 1 through 7 )
2X-RAY DIFFRACTION2chain 'E' and (resid 8 through 17 )
3X-RAY DIFFRACTION3chain 'E' and (resid 18 through 32 )
4X-RAY DIFFRACTION4chain 'E' and (resid 33 through 39 )
5X-RAY DIFFRACTION5chain 'E' and (resid 40 through 51 )
6X-RAY DIFFRACTION6chain 'E' and (resid 52 through 72 )
7X-RAY DIFFRACTION7chain 'E' and (resid 73 through 82 )
8X-RAY DIFFRACTION8chain 'E' and (resid 83 through 98 )
9X-RAY DIFFRACTION9chain 'E' and (resid 99 through 113 )
10X-RAY DIFFRACTION10chain 'E' and (resid 114 through 120 )

+
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