[English] 日本語
Yorodumi
- PDB-6yxk: Crystal structure of ACPA 3F3 in complex with cit-vimentin 59-74 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yxk
TitleCrystal structure of ACPA 3F3 in complex with cit-vimentin 59-74
Components
  • ACPA 3F3 Fab fragment - heavy chain
  • ACPA 3F3 Fab fragment - light chain
  • Citrullinated Vimentin (59-74)
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody Fab fragment / citrullinated vimentin
Function / homology
Function and homology information


keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament / microtubule organizing center ...keratin filament binding / lens fiber cell development / intermediate filament organization / cellular response to muramyl dipeptide / structural constituent of eye lens / astrocyte development / Striated Muscle Contraction / RHOBTB1 GTPase cycle / intermediate filament / microtubule organizing center / intermediate filament cytoskeleton / cell leading edge / Bergmann glial cell differentiation / positive regulation of collagen biosynthetic process / Caspase-mediated cleavage of cytoskeletal proteins / phagocytic vesicle / regulation of mRNA stability / Late endosomal microautophagy / structural constituent of cytoskeleton / nuclear matrix / Aggrephagy / cellular response to type II interferon / Chaperone Mediated Autophagy / peroxisome / neuron projection development / double-stranded RNA binding / negative regulation of neuron projection development / scaffold protein binding / Interleukin-4 and Interleukin-13 signaling / cellular response to lipopolysaccharide / molecular adaptor activity / cytoskeleton / axon / protein domain specific binding / focal adhesion / positive regulation of gene expression / extracellular exosome / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Intermediate filament head, DNA-binding domain / Intermediate filament head (DNA binding) region / Intermediate filament protein, conserved site / Intermediate filament protein / Intermediate filament (IF) rod domain signature. / Intermediate filament, rod domain / Intermediate filament (IF) rod domain profile. / Intermediate filament protein
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGe, C. / Holmdahl, R.
Funding support Sweden, 2items
OrganizationGrant numberCountry
Swedish Research Council Sweden
Knut and Alice Wallenberg Foundation Sweden
CitationJournal: Sci Adv / Year: 2022
Title: Surface Ig variable domain glycosylation affects autoantigen binding and acts as threshold for human autoreactive B cell activation.
Authors: Kissel, T. / Ge, C. / Hafkenscheid, L. / Kwekkeboom, J.C. / Slot, L.M. / Cavallari, M. / He, Y. / van Schie, K.A. / Vergroesen, R.D. / Kampstra, A.S.B. / Reijm, S. / Stoeken-Rijsbergen, G. / ...Authors: Kissel, T. / Ge, C. / Hafkenscheid, L. / Kwekkeboom, J.C. / Slot, L.M. / Cavallari, M. / He, Y. / van Schie, K.A. / Vergroesen, R.D. / Kampstra, A.S.B. / Reijm, S. / Stoeken-Rijsbergen, G. / Koeleman, C. / Voortman, L.M. / Heitman, L.H. / Xu, B. / Pruijn, G.J.M. / Wuhrer, M. / Rispens, T. / Huizinga, T.W.J. / Scherer, H.U. / Reth, M. / Holmdahl, R. / Toes, R.E.M.
History
DepositionMay 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 12, 2021Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / chem_comp_atom / chem_comp_bond / pdbx_validate_close_contact / pdbx_validate_main_chain_plane / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 2.1Jan 24, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ACPA 3F3 Fab fragment - heavy chain
B: ACPA 3F3 Fab fragment - light chain
C: Citrullinated Vimentin (59-74)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2696
Polymers49,6053
Non-polymers6643
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-4 kcal/mol
Surface area20320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.379, 82.094, 135.613
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody ACPA 3F3 Fab fragment - heavy chain


Mass: 23772.783 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCEP4 / Cell line (production host): Expi 293F(TM) / Production host: Homo sapiens (human)
#2: Antibody ACPA 3F3 Fab fragment - light chain


Mass: 24120.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pCEP4 / Cell line (production host): Expi 293F(TM) / Production host: Homo sapiens (human)
#3: Protein/peptide Citrullinated Vimentin (59-74)


Mass: 1711.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P08670
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20mM Tris pH 7.5, 20mM NaCl, 0.2M ammonium chloride pH 6.3, (20%) w/v PEG 3350)

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9184 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2→52.334 Å / Num. obs: 40933 / % possible obs: 99.5 % / Redundancy: 8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.067 / Rrim(I) all: 0.14 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.94-52.286.90.0585420.9960.0320.066
2-2.058.20.93630180.6760.5111.069

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
XDS0.7.4data reduction
Cootmodel building
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5OCX(early model)

5ocx


Resolution: 2→52.28 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.931 / SU B: 9.327 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.17 / ESU R Free: 0.161
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2534 2026 4.953 %
Rwork0.2105 38876 -
all0.213 --
obs-40902 99.513 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 33.325 Å2
Baniso -1Baniso -2Baniso -3
1--0.926 Å20 Å2-0 Å2
2---1.275 Å20 Å2
3---2.201 Å2
Refinement stepCycle: LAST / Resolution: 2→52.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3395 0 64 303 3762
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0133546
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173151
X-RAY DIFFRACTIONr_angle_refined_deg2.2591.6654819
X-RAY DIFFRACTIONr_angle_other_deg1.4721.5977356
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.145439
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.06923.66153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.78615546
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9681511
X-RAY DIFFRACTIONr_chiral_restr0.0930.2469
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.023939
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02728
X-RAY DIFFRACTIONr_nbd_refined0.240.2631
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2110.23066
X-RAY DIFFRACTIONr_nbtor_refined0.1820.21711
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0980.21823
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.2289
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2530.214
X-RAY DIFFRACTIONr_nbd_other0.2720.239
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2050.29
X-RAY DIFFRACTIONr_mcbond_it1.3441.671774
X-RAY DIFFRACTIONr_mcbond_other1.3441.6691773
X-RAY DIFFRACTIONr_mcangle_it2.0512.492207
X-RAY DIFFRACTIONr_mcangle_other2.0512.4922208
X-RAY DIFFRACTIONr_scbond_it1.8421.8771772
X-RAY DIFFRACTIONr_scbond_other1.8381.8771772
X-RAY DIFFRACTIONr_scangle_it2.8212.7312612
X-RAY DIFFRACTIONr_scangle_other2.8212.7312613
X-RAY DIFFRACTIONr_lrange_it7.16821.3673907
X-RAY DIFFRACTIONr_lrange_other7.06520.6453845
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.0520.2851510.2612866X-RAY DIFFRACTION99.8015
2.052-2.1080.3051480.262722X-RAY DIFFRACTION99.6874
2.108-2.1690.3311550.2662687X-RAY DIFFRACTION99.8595
2.169-2.2360.3421450.2982605X-RAY DIFFRACTION99.6016
2.236-2.3090.3081170.2842548X-RAY DIFFRACTION99.7754
2.309-2.390.3331260.2592464X-RAY DIFFRACTION99.6921
2.39-2.480.3071220.2342363X-RAY DIFFRACTION99.5194
2.48-2.5810.2711100.2112284X-RAY DIFFRACTION98.6403
2.581-2.6960.2851310.1922152X-RAY DIFFRACTION98.2781
2.696-2.8270.216790.1872097X-RAY DIFFRACTION97.4038
2.827-2.980.2411070.2012001X-RAY DIFFRACTION99.8579
2.98-3.160.231050.2021911X-RAY DIFFRACTION99.9504
3.16-3.3780.219950.1971793X-RAY DIFFRACTION99.8942
3.378-3.6480.2281050.1981653X-RAY DIFFRACTION99.9431
3.648-3.9950.237740.1931563X-RAY DIFFRACTION99.9389
3.995-4.4650.218760.1751428X-RAY DIFFRACTION100
4.465-5.1520.265680.1771257X-RAY DIFFRACTION100
5.152-6.3020.232410.2291096X-RAY DIFFRACTION100
6.302-8.8760.238480.204869X-RAY DIFFRACTION99.8911
8.876-52.280.23230.23517X-RAY DIFFRACTION99.2647
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)
11.5688-0.79380.70031.4885-0.50570.8003-0.0541-0.04350.17570.0438-0.0148-0.0868-0.0944-0.04290.06890.2158-0.0299-0.0010.2182-0.01110.020114.439965.370723.87
20.8521-0.84140.72491.2336-0.97111.0330.05660.0283-0.0825-0.05380.03390.12170.0083-0.0437-0.09050.2272-0.033-0.00580.2461-0.00940.01284.166254.393313.8032
30.0358-0.46560.21338.3666-2.39011.3503-0.00210.04110.0170.0197-0.0375-0.44070.01990.31120.03970.17060.0063-0.00870.18410.01950.169430.769835.847432.792
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLA2 - 401
2X-RAY DIFFRACTION2ALLB1 - 301
3X-RAY DIFFRACTION3ALLC1 - 9

+
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