[English] 日本語
Yorodumi
- PDB-6yxm: Crystal structure of ACPA 1F2 in complex with CII-C-39-CIT -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6yxm
TitleCrystal structure of ACPA 1F2 in complex with CII-C-39-CIT
Components
  • (ACPA 1F2 Fab fragment - ...) x 2
  • CII-C-39-CIT
KeywordsIMMUNE SYSTEM / anti-citrullinated protein antibody / collagen type II
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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 2.0Dec 7, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / atom_type / entity / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / pdbx_validate_symm_contact / struct_asym / struct_conn / struct_ref / struct_ref_seq
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_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.pdbx_label_seq_id / _atom_site_anisotrop.type_symbol / _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Revision 3.0Nov 15, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
Revision 3.1Jan 31, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
BBB: CII-C-39-CIT
HHH: ACPA 1F2 Fab fragment - heavy chain
LLL: ACPA 1F2 Fab fragment - light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5608
Polymers47,5663
Non-polymers9945
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-115 kcal/mol
Surface area19850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.010, 89.650, 118.680
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
Antibody , 2 types, 2 molecules HHHLLL

#2: Antibody ACPA 1F2 Fab fragment - heavy chain


Mass: 23550.391 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody ACPA 1F2 Fab fragment - light chain


Mass: 23044.248 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Protein/peptide / Sugars , 2 types, 2 molecules BBB

#1: Protein/peptide CII-C-39-CIT


Mass: 971.051 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE

-
Non-polymers , 2 types, 37 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: Zn
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.95 Å3/Da / Density % sol: 58.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20mM Tris pH 7.4, 20mMNaCl, 20% (w/v) PEG 6000, 0.1M HEPES 7.0 pH 7.0, 0.01M zinc chloride.

-
Data collection

DiffractionMean temperature: 210 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97662 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97662 Å / Relative weight: 1
ReflectionResolution: 2.85→118.75 Å / Num. obs: 13893 / % possible obs: 99.9 % / Redundancy: 8.8 % / CC1/2: 0.993 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.076 / Rrim(I) all: 0.165 / Net I/σ(I): 9.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9.01-118.757.70.0745150.9960.0390.084
2.85-38.70.50119760.9140.2670.569

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
REFMAC5.8.0258refinement
Aimlessdata reduction
XDSdata reduction
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ocx

5ocx


Resolution: 2.85→36.219 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.877 / SU B: 30.017 / SU ML: 0.283 / Cross valid method: FREE R-VALUE / ESU R Free: 0.412
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2762 638 4.712 %
Rwork0.2098 --
all0.213 --
obs-13539 98.137 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 39.044 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å2-0 Å2
2--0.63 Å20 Å2
3---0.18 Å2
Refinement stepCycle: LAST / Resolution: 2.85→36.219 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3275 0 64 33 3372
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0133425
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173009
X-RAY DIFFRACTIONr_angle_refined_deg1.3331.6694660
X-RAY DIFFRACTIONr_angle_other_deg1.1221.5937023
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.1235427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.40722.448143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.44615512
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.1541514
X-RAY DIFFRACTIONr_chiral_restr0.0440.2467
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023790
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02706
X-RAY DIFFRACTIONr_nbd_refined0.1850.2489
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1740.22648
X-RAY DIFFRACTIONr_nbtor_refined0.1590.21588
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.21678
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1170.278
X-RAY DIFFRACTIONr_metal_ion_refined0.1070.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2670.218
X-RAY DIFFRACTIONr_nbd_other0.2730.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1180.22
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1120.23
X-RAY DIFFRACTIONr_mcbond_it0.6462.9721726
X-RAY DIFFRACTIONr_mcbond_other0.6452.9721725
X-RAY DIFFRACTIONr_mcangle_it1.1434.4572147
X-RAY DIFFRACTIONr_mcangle_other1.1434.4572148
X-RAY DIFFRACTIONr_scbond_it0.6563.0491699
X-RAY DIFFRACTIONr_scbond_other0.6563.0491700
X-RAY DIFFRACTIONr_scangle_it1.0454.5442513
X-RAY DIFFRACTIONr_scangle_other1.0444.5442514
X-RAY DIFFRACTIONr_lrange_it2.34833.4893441
X-RAY DIFFRACTIONr_lrange_other2.34533.4743440
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.9240.357540.259939X-RAY DIFFRACTION98.6097
2.924-3.0040.313450.276905X-RAY DIFFRACTION98.9583
3.004-3.0910.252440.251916X-RAY DIFFRACTION99.4819
3.091-3.1860.299380.239856X-RAY DIFFRACTION98.7845
3.186-3.290.444380.242851X-RAY DIFFRACTION98.8876
3.29-3.4050.294330.217811X-RAY DIFFRACTION98.3683
3.405-3.5330.276460.217793X-RAY DIFFRACTION98.5899
3.533-3.6770.244340.207740X-RAY DIFFRACTION98.2234
3.677-3.840.27350.21732X-RAY DIFFRACTION98.3333
3.84-4.0270.358410.212700X-RAY DIFFRACTION98.2759
4.027-4.2440.267250.19675X-RAY DIFFRACTION98.3146
4.244-4.5010.199350.173630X-RAY DIFFRACTION98.8113
4.501-4.810.21320.157604X-RAY DIFFRACTION97.6959
4.81-5.1940.252330.172535X-RAY DIFFRACTION97.7625
5.194-5.6860.312270.201516X-RAY DIFFRACTION97.4865
5.686-6.3520.249190.211462X-RAY DIFFRACTION96.3928
6.352-7.3260.398190.196416X-RAY DIFFRACTION97.0982
7.326-8.9490.221150.175373X-RAY DIFFRACTION97.2431
8.949-12.5570.226150.205276X-RAY DIFFRACTION94.7883
12.557-36.2190.342100.334171X-RAY DIFFRACTION90.5
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)
10.6819-0.13611.09850.043-0.23221.79480.05070.1869-0.0849-0.00240.0156-0.00660.08350.2751-0.06630.20180.01120.08450.257-0.05530.25426.073214.951323.9391
20.62-0.2441-0.13234.3543-0.52820.7875-0.0258-0.00730.04240.0341-0.00940.2153-0.1051-0.12940.03520.0272-0.0068-0.02740.11620.02080.06925.83540.45915.7579
30.3634-0.68740.1152.9820.23370.173-0.0461-0.0206-0.0247-0.18620.02380.0238-0.0754-0.00740.02240.0590.00210.03270.04070.02730.100921.638743.980612.7694
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLBBB597 - 605
2X-RAY DIFFRACTION2ALLHHH1 - 230
3X-RAY DIFFRACTION3ALLLLL1 - 212

+
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://pdbjlc1.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