[English] 日本語
Yorodumi
- PDB-8xs1: Crystal structure of Fab fragment of anti-osteocalcin antibody KT... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8xs1
TitleCrystal structure of Fab fragment of anti-osteocalcin antibody KTM219 complexed with C-terminal peptide antigen
Components
  • Heavy chain fragment (Fd) chain of anti-osteocalcin antibody KTM219
  • Light chain of anti-osteocalcin antibody KTM219
  • Osteocalcin
KeywordsIMMUNE SYSTEM / Antibody / Immunoglobulin fold / Osteocalcin / Quenchbody (Q-body) / Open sandwich immunoassay
Function / homology
Function and homology information


structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / response to macrophage colony-stimulating factor / regulation of testosterone biosynthetic process / response to gravity / response to vitamin K / regulation of osteoclast differentiation / cellular response to zinc ion starvation / type B pancreatic cell proliferation ...structural constituent of bone / hydroxyapatite binding / negative regulation of bone development / response to macrophage colony-stimulating factor / regulation of testosterone biosynthetic process / response to gravity / response to vitamin K / regulation of osteoclast differentiation / cellular response to zinc ion starvation / type B pancreatic cell proliferation / cellular response to vitamin D / regulation of bone mineralization / response to vitamin D / regulation of bone resorption / osteoblast development / response to hydroxyisoflavone / positive regulation of neurotransmitter secretion / response to zinc ion / bone mineralization / RUNX2 regulates osteoblast differentiation / response to testosterone / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Gamma-carboxylation of protein precursors / Removal of aminoterminal propeptides from gamma-carboxylated proteins / response to glucocorticoid / response to mechanical stimulus / regulation of cellular response to insulin stimulus / response to activity / skeletal system development / stem cell differentiation / brain development / cellular response to growth factor stimulus / hormone activity / bone development / Golgi lumen / cognition / cellular response to insulin stimulus / response to estrogen / osteoblast differentiation / glucose homeostasis / vesicle / perikaryon / response to ethanol / learning or memory / cell adhesion / endoplasmic reticulum lumen / response to xenobiotic stimulus / dendrite / calcium ion binding / structural molecule activity / extracellular space / extracellular region / cytoplasm
Similarity search - Function
Osteocalcin/matrix Gla protein / Osteocalcin / Gamma-carboxyglutamic acid-rich (GLA) domain / Gamma-carboxyglutamic acid-rich (GLA) domain superfamily / Vitamin K-dependent carboxylation domain. / Gla domain profile. / Domain containing Gla (gamma-carboxyglutamate) residues.
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKomatsu, M. / Dong, J. / Ueda, H. / Arai, R.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science (JSPS)JP19H02522, JP17KK0104, JP16K05841, JP16H00761, JP24780097, JP15H04191, JP18H03851, JP24K01267 Japan
Ministry of Education, Culture, Sports, Science and Technology (Japan)Cooperative Research Program of Network Joint Research Center for Materials and Devices Japan
Citation
Journal: Int J Mol Sci / Year: 2025
Title: Crystal Structures of Antigen-Binding Fragment of Anti-Osteocalcin Antibody KTM219.
Authors: Yazaki, S. / Komatsu, M. / Dong, J. / Ueda, H. / Arai, R.
#1: Journal: Sci Rep / Year: 2014
Title: Ultra Q-bodies: quench-based antibody probes that utilize dye-dye interactions with enhanced antigen-dependent fluorescence.
Authors: Abe, R. / Jeong, H.J. / Arakawa, D. / Dong, J. / Ohashi, H. / Kaigome, R. / Saiki, F. / Yamane, K. / Takagi, H. / Ueda, H.
#2: Journal: Sensors (Basel) / Year: 2021
Title: Recent Advances in Quenchbody, a Fluorescent Immunosensor.
Authors: Dong, J. / Ueda, H.
#3: Journal: Anal Chem / Year: 2007
Title: Noncompetitive detection of low molecular weight peptides by open sandwich immunoassay.
Authors: Lim, S.L. / Ichinose, H. / Shinoda, T. / Ueda, H.
History
DepositionJan 8, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2025Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: Heavy chain fragment (Fd) chain of anti-osteocalcin antibody KTM219
L: Light chain of anti-osteocalcin antibody KTM219
A: Osteocalcin


Theoretical massNumber of molelcules
Total (without water)52,3593
Polymers52,3593
Non-polymers00
Water2,306128
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4680 Å2
ΔGint-29 kcal/mol
Surface area19540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.880, 67.489, 138.655
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody Heavy chain fragment (Fd) chain of anti-osteocalcin antibody KTM219


Mass: 26202.979 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HYBRIDOMA KTM-219 / Plasmid: pET-Fab(KTM219) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY
#2: Antibody Light chain of anti-osteocalcin antibody KTM219


Mass: 25259.844 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: HYBRIDOMA KTM-219 / Plasmid: pET-Fab(KTM219) / Production host: Escherichia coli (E. coli) / Strain (production host): SHuffle T7 Express lysY
#3: Protein/peptide Osteocalcin / Bone Gla protein / BGP / Gamma-carboxyglutamic acid-containing protein


Mass: 896.048 Da / Num. of mol.: 1 / Fragment: C-terminal peptide (43-49) antigen / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P02818
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.26 % / Description: Plate-like crystal
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 3.4
Details: 0.07 M Citric acid, 0.03 M BIS-TRIS propane, 16% Polyethylene glycol 3,350, by using random Microseed Matrix Screening (rMMS) method

-
Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 19, 2015
RadiationMonochromator: Numerical link type Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 18912 / % possible obs: 99.1 % / Redundancy: 6.1 % / Rmerge(I) obs: 0.151 / Rpim(I) all: 0.066 / Rrim(I) all: 0.165 / Net I/av σ(I): 10.6 / Net I/σ(I): 5.3
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.3-2.386.50.7692.618340.8360.9540.320.8351.00399.6
2.38-2.486.40.6832.8818590.8820.9680.2870.7431.01799.4
2.48-2.596.30.563.318860.9160.9780.2370.610.99899.4
2.59-2.736.30.444.0318610.9470.9860.1860.4790.99599.4
2.73-2.96.20.3714.4818600.940.9840.1590.4051.00399.2
2.9-3.126.10.2576.0218630.9670.9920.1110.281198.7
3.12-3.4460.1669.4318770.9770.9940.0720.1821.01898.5
3.44-3.935.80.1181218810.9850.9960.0530.131.0298.1
3.93-4.955.60.08316.719270.9920.9980.0380.0921.01499.1
4.95-505.80.07321.720640.9940.9980.0330.0811.02199.4

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5X5X

5x5x


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 8.847 / SU ML: 0.206 / Cross valid method: THROUGHOUT / ESU R: 0.429 / ESU R Free: 0.255 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24781 984 5.2 %RANDOM
Rwork0.19897 ---
obs0.20143 17875 98.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.498 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å20 Å20 Å2
2--1.69 Å20 Å2
3---1.68 Å2
Refinement stepCycle: 1 / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3319 0 0 128 3447
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193402
X-RAY DIFFRACTIONr_bond_other_d0.0060.023108
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9494626
X-RAY DIFFRACTIONr_angle_other_deg0.97937214
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4895435
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.26724.729129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.19315544
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.208158
X-RAY DIFFRACTIONr_chiral_restr0.0870.2522
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213844
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02754
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4863.8211749
X-RAY DIFFRACTIONr_mcbond_other2.4873.8221748
X-RAY DIFFRACTIONr_mcangle_it3.8955.722181
X-RAY DIFFRACTIONr_mcangle_other3.8945.7192182
X-RAY DIFFRACTIONr_scbond_it2.8734.081653
X-RAY DIFFRACTIONr_scbond_other2.8724.081653
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6565.9732445
X-RAY DIFFRACTIONr_long_range_B_refined7.40330.5193658
X-RAY DIFFRACTIONr_long_range_B_other7.40130.5173658
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.357 Å
RfactorNum. reflection% reflection
Rfree0.342 65 -
Rwork0.284 1268 -
obs--96.59 %

+
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