[English] 日本語
Yorodumi
- PDB-9uds: Single-chain Fv antibody of C6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9uds
TitleSingle-chain Fv antibody of C6
ComponentsSingle-chain Fv antibody of C6
KeywordsIMMUNE SYSTEM / ANTIGEN BINDING / AFFINITY MATURATION / SOMATIC HYPERMUTATION
Function / homologyISOPROPYL ALCOHOL
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsYoshida, M. / Hanazono, Y. / Numoto, N. / Ito, N. / Oda, M.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Structural basis of anti-(4-hydroxy-3-nitrophenyl)acetyl antibodies during affinity maturation
Authors: Yoshida, M. / Hanazono, Y. / Numoto, N. / Yabuno, S. / Ito, N. / Azuma, T. / Oda, M.
History
DepositionApr 7, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Single-chain Fv antibody of C6
B: Single-chain Fv antibody of C6
C: Single-chain Fv antibody of C6
D: Single-chain Fv antibody of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,8649
Polymers104,4684
Non-polymers3965
Water11,494638
1
A: Single-chain Fv antibody of C6


Theoretical massNumber of molelcules
Total (without water)26,1171
Polymers26,1171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10440 Å2
MethodPISA
2
B: Single-chain Fv antibody of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,2693
Polymers26,1171
Non-polymers1522
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-2 kcal/mol
Surface area10590 Å2
MethodPISA
3
C: Single-chain Fv antibody of C6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3614
Polymers26,1171
Non-polymers2443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-2 kcal/mol
Surface area10550 Å2
MethodPISA
4
D: Single-chain Fv antibody of C6


Theoretical massNumber of molelcules
Total (without water)26,1171
Polymers26,1171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area10590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)121.236, 116.853, 59.860
Angle α, β, γ (deg.)90.000, 90.709, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

-
Components

#1: Antibody
Single-chain Fv antibody of C6


Mass: 26116.920 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 638 / 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: 2.03 Å3/Da / Density % sol: 39.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-propanol, 20% w/v polyethylene glycol 4,000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Oct 12, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→50 Å / Num. obs: 57203 / % possible obs: 99.7 % / Redundancy: 13.8 % / Biso Wilson estimate: 28.93 Å2 / Rmerge(I) obs: 0.458 / Net I/σ(I): 8.8
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 2.356 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5661 / CC1/2: 0.518 / % possible all: 98.6

-
Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.97 Å / SU ML: 0.2339 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.4198
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2153 2873 5.02 %
Rwork0.1787 54330 -
obs0.1805 57203 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.66 Å2
Refinement stepCycle: LAST / Resolution: 1.99→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 26 638 7668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00397229
X-RAY DIFFRACTIONf_angle_d0.72829845
X-RAY DIFFRACTIONf_chiral_restr0.04881082
X-RAY DIFFRACTIONf_plane_restr0.00561246
X-RAY DIFFRACTIONf_dihedral_angle_d15.27062514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.020.33021470.26282508X-RAY DIFFRACTION97.57
2.02-2.050.27311170.24332613X-RAY DIFFRACTION99.67
2.05-2.090.29081380.23722528X-RAY DIFFRACTION99.22
2.09-2.130.29011320.2262582X-RAY DIFFRACTION99.6
2.13-2.170.251310.22812589X-RAY DIFFRACTION99.45
2.17-2.220.30741470.22082568X-RAY DIFFRACTION99.38
2.22-2.270.27411330.22352580X-RAY DIFFRACTION100
2.27-2.330.31821240.22112585X-RAY DIFFRACTION99.45
2.33-2.390.29921470.21282581X-RAY DIFFRACTION99.67
2.39-2.460.25931320.20312586X-RAY DIFFRACTION99.96
2.46-2.540.24611320.1952566X-RAY DIFFRACTION99.74
2.54-2.630.23731440.18972618X-RAY DIFFRACTION99.86
2.63-2.740.23241300.18822573X-RAY DIFFRACTION99.89
2.74-2.860.24141410.19182607X-RAY DIFFRACTION99.96
2.86-3.020.25111390.1822589X-RAY DIFFRACTION100
3.02-3.20.22241370.17852590X-RAY DIFFRACTION100
3.2-3.450.20641420.16322601X-RAY DIFFRACTION100
3.45-3.80.20351380.14892601X-RAY DIFFRACTION100
3.8-4.350.14531420.13772598X-RAY DIFFRACTION100
4.35-5.480.14561380.13832615X-RAY DIFFRACTION99.96
5.48-48.970.18541420.18382652X-RAY DIFFRACTION99.89

+
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