[English] 日本語
Yorodumi
- PDB-6sf6: Crystal structure of the mAb 15A in complex with COMP-epitope P6 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6sf6
TitleCrystal structure of the mAb 15A in complex with COMP-epitope P6
Components
  • (COMP-reactive monoclonal antibody 15A Fab fragment, ...) x 2
  • P6 epitope of cartilage oligomeric matrix protein (COMP)
KeywordsIMMUNE SYSTEM / cartilage oligomeric matrix protein / autoantibody / arthrogenicity / ACPA
Function / homology
Function and homology information


cartilage homeostasis / Integrin cell surface interactions / tendon development / negative regulation of hemostasis / ECM proteoglycans / musculoskeletal movement / vascular associated smooth muscle contraction / vascular associated smooth muscle cell development / bone growth / chondrocyte development ...cartilage homeostasis / Integrin cell surface interactions / tendon development / negative regulation of hemostasis / ECM proteoglycans / musculoskeletal movement / vascular associated smooth muscle contraction / vascular associated smooth muscle cell development / bone growth / chondrocyte development / BMP binding / chondrocyte proliferation / endochondral bone growth / growth plate cartilage development / vitamin D binding / positive regulation of chondrocyte proliferation / muscle cell development / regulation of bone mineralization / heparan sulfate proteoglycan binding / collagen fibril organization / bone morphogenesis / cartilage development / limb development / proteoglycan binding / neuromuscular process / artery morphogenesis / skin development / extracellular matrix structural constituent / bone mineralization / fibronectin binding / response to unfolded protein / protein secretion / BMP signaling pathway / collagen binding / ossification / skeletal system development / protein homooligomerization / multicellular organism growth / protein processing / platelet aggregation / cellular senescence / blood coagulation / integrin binding / heparin binding / regulation of gene expression / collagen-containing extracellular matrix / protease binding / apoptotic process / calcium ion binding / negative regulation of apoptotic process / protein-containing complex / extracellular space / extracellular region
Similarity search - Function
: / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat ...: / Thrombospondin/cartilage oligomeric matrix protein, coiled-coil domain / Thrombospondin-5, coiled coil region / Cartilage oligomeric matrix protein / Thrombospondin, C-terminal / Thrombospondin, type 3 repeat / Thrombospondin C-terminal region / Thrombospondin type-3 (TSP3) repeat profile. / Thrombospondin C-terminal domain profile. / Thrombospondin, type 3-like repeat / Thrombospondin type 3 repeat / TSP type-3 repeat / : / Calcium-binding EGF domain / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / EGF-like domain / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Cartilage oligomeric matrix protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsDobritzsch, D. / Ge, C. / Holmdahl, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2010.0148 Sweden
Swedish Research CouncilK2011-52X-07931-25-5, K2009-75SX-21029-01-3, K2012-75SX-22072-01-3, 2015-02662 Sweden
CitationJournal: To Be Published
Title: Antibodies to cartilage oligomeric matrix protein in vivo are pathogenic and clinically relevant in rheumatoid arthritis
Authors: Ge, C. / Tong, D. / Loennblom, E. / Bibo, L. / Hagert, C. / Kastbom, A. / Gjertsson, I. / Dobritzsch, D. / Holmdahl, R.
History
DepositionAug 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 24, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
H: COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain
L: COMP-reactive monoclonal antibody 15A Fab fragment, light chain
A: COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain
B: COMP-reactive monoclonal antibody 15A Fab fragment, light chain
C: P6 epitope of cartilage oligomeric matrix protein (COMP)
D: P6 epitope of cartilage oligomeric matrix protein (COMP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,23814
Polymers103,4936
Non-polymers7458
Water10,881604
1
H: COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain
L: COMP-reactive monoclonal antibody 15A Fab fragment, light chain
C: P6 epitope of cartilage oligomeric matrix protein (COMP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,3079
Polymers51,7473
Non-polymers5616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-45 kcal/mol
Surface area19580 Å2
MethodPISA
2
A: COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain
B: COMP-reactive monoclonal antibody 15A Fab fragment, light chain
D: P6 epitope of cartilage oligomeric matrix protein (COMP)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,9315
Polymers51,7473
Non-polymers1842
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-41 kcal/mol
Surface area19720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.174, 84.421, 151.885
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Protein/peptide , 1 types, 2 molecules CD

#3: Protein/peptide P6 epitope of cartilage oligomeric matrix protein (COMP)


Mass: 2120.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: COMP protein P6 epitope / Source: (synth.) Rattus norvegicus (Norway rat) / References: UniProt: P35444*PLUS

-
Antibody , 2 types, 4 molecules HALB

#1: Antibody COMP-reactive monoclonal antibody 15A Fab fragment, heavy chain


Mass: 25390.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridomas / Production host: Mus musculus (house mouse)
#2: Antibody COMP-reactive monoclonal antibody 15A Fab fragment, light chain


Mass: 24235.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): B cell hybridomas / Production host: Mus musculus (house mouse)

-
Non-polymers , 3 types, 612 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 604 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 30% polyethylene glycol 8000, 0.2 M ammonium sulphate 10 mg/ml 15A Fab fragment + P6 peptide (molar ratio 1:1.2) in 20 mM Tris HCl pH 7.4, 50 mM NaCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 10, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.9→84.42 Å / Num. obs: 80712 / % possible obs: 98.9 % / Redundancy: 3.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.062 / Rpim(I) all: 0.034 / Rrim(I) all: 0.071 / Net I/σ(I): 12.6 / Num. measured all: 318137 / Scaling rejects: 125
Reflection shellResolution: 1.9→1.94 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.539 / Num. unique obs: 4597 / CC1/2: 0.731 / Rpim(I) all: 0.292 / Rrim(I) all: 0.617 / % possible all: 99.3

-
Processing

Software
NameVersionClassification
Aimless0.2.17data scaling
REFMAC5.8.0069refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IQW, 2IPT

1iqw

2ipt


Resolution: 1.9→84 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.955 / SU B: 6.777 / SU ML: 0.099 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.137 / ESU R Free: 0.124
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2031 3924 4.9 %RANDOM
Rwork0.1738 ---
obs0.1752 76757 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 115.56 Å2 / Biso mean: 37.924 Å2 / Biso min: 13.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.32 Å2-0 Å2-0 Å2
2---1.44 Å20 Å2
3---1.76 Å2
Refinement stepCycle: final / Resolution: 1.9→84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6892 0 46 608 7546
Biso mean--53.68 40.86 -
Num. residues----888
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.027206
X-RAY DIFFRACTIONr_bond_other_d0.0040.026517
X-RAY DIFFRACTIONr_angle_refined_deg1.3011.9499847
X-RAY DIFFRACTIONr_angle_other_deg0.95315111
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2035918
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82724.324296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.809151129
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0921526
X-RAY DIFFRACTIONr_chiral_restr0.0750.21105
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0218159
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021647
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 326 -
Rwork0.255 5623 -
all-5949 -
obs--99.12 %
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)
10.53720.29790.72956.64791.36971.54150.03720.03250.0087-0.4418-0.03180.09730.0264-0.0538-0.00540.05190.00510.01780.030.02880.0685126.8531-24.575660.3259
20.86860.6020.76022.31971.24662.01710.07810.02750.0476-0.1192-0.1022-0.11390.0573-0.03660.02410.02560.01310.02010.01050.01290.0192125.3653-26.123262.3935
36.655-1.61481.72771.19460.521.63970.11720.54430.1509-0.2437-0.22430.0857-0.1236-0.02650.10710.28540.0368-0.05380.14860.06470.114109.0813-31.797441.8165
44.10630.07960.5541.3132-0.24210.7225-0.0281-0.06710.01920.02980.03220.0906-0.1123-0.1156-0.00410.03670.01370.01630.0199-0.00390.0208109.4409-16.111271.9789
50.7173-1.446-0.4375.74333.89964.54080.0703-0.0074-0.31370.1005-0.2060.54670.5814-0.19280.13570.21710.0166-0.08230.203-0.05140.239196.0803-39.327847.4041
60.916-1.4377-0.7646.54154.38034.06080.12250.09-0.2747-0.138-0.37130.57280.3146-0.52670.24880.28440.0085-0.08410.2333-0.04660.281894.5632-40.848944.7707
71.41270.54980.31474.86021.00991.0972-0.0127-0.0117-0.0625-0.1332-0.0327-0.03440.0960.00650.04550.02280.00670.0130.01050.01050.0151125.354117.174663.4704
84.2746-1.53831.15613.4858-0.22752.7910.06730.1334-0.124-0.3943-0.07020.35150.0819-0.35070.00290.25960.0043-0.04290.1516-0.04610.0518106.058710.670540.9821
94.57110.8449-0.48861.6667-0.30230.83270.0089-0.11420.29930.02890.03960.267-0.1443-0.1448-0.04850.05410.01820.01660.04050.00060.086107.191227.260272.4627
101.3670.1820.45111.42170.63393.1293-0.00350.1612-0.0311-0.3395-0.03720.36580.1202-0.64910.04070.1257-0.0356-0.06990.2010.02910.1483100.442114.855.7801
112.1045-1.4993-0.67526.13994.52035.9621-0.00690.0471-0.8271-0.0612-0.30640.74430.7827-1.09360.31330.4385-0.2084-0.08310.57660.02370.521590.791.907145.7469
126.92961.05910.69163.3109-0.9153.8865-0.1043-0.18690.17740.0431-0.0086-0.23-0.20060.09350.11290.10480.0118-0.00460.1202-0.01020.1279133.170529.467475.9101
1310.6417-0.70010.88315.85730.16069.0276-0.1389-0.27610.34950.2398-0.0112-0.3945-0.62940.49830.15010.0783-0.0112-0.01940.06040.00560.1406135.5627-12.062276.5247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 43
2X-RAY DIFFRACTION2A44 - 145
3X-RAY DIFFRACTION3A146 - 222
4X-RAY DIFFRACTION4B1 - 109
5X-RAY DIFFRACTION5B110 - 167
6X-RAY DIFFRACTION6B168 - 218
7X-RAY DIFFRACTION7H1 - 124
8X-RAY DIFFRACTION8H125 - 222
9X-RAY DIFFRACTION9L1 - 81
10X-RAY DIFFRACTION10L82 - 144
11X-RAY DIFFRACTION11L145 - 216
12X-RAY DIFFRACTION12C242 - 252
13X-RAY DIFFRACTION13D242 - 252

+
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