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- PDB-2j6e: Crystal Structure of an Autoimmune Complex between a Human IgM Rh... -

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Basic information

Entry
Database: PDB / ID: 2j6e
TitleCrystal Structure of an Autoimmune Complex between a Human IgM Rheumatoid Factor and IgG1 Fc reveals a Novel Fc Epitope and Evidence for Affinity Maturation
Components
  • (IGM) x 2
  • IG GAMMA-1 CHAIN C REGION
KeywordsIMMUNE SYSTEM / AUTOIMMUNE COMPLEX HUMAN IGM RHEUMATOID FACTOR IGG1-FC / IMMUNOGLOBULIN C REGION / MEMBRANE / GLYCOPROTEIN / TRANSMEMBRANE / HYPOTHETICAL PROTEIN / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / CACODYLATE ION / : / Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsDuquerroy, S. / Stura, E.A. / Bressanelli, S. / Browne, H. / Beale, D. / Hamon, M. / Casali, P. / Vaney, M.C. / Rey, F.A. / Sutton, B.J. / Taussig, M.J.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Crystal structure of a human autoimmune complex between IgM rheumatoid factor RF61 and IgG1 Fc reveals a novel epitope and evidence for affinity maturation.
Authors: Duquerroy, S. / Stura, E.A. / Bressanelli, S. / Fabiane, S.M. / Vaney, M.C. / Beale, D. / Hamon, M. / Casali, P. / Rey, F.A. / Sutton, B.J. / Taussig, M.J.
History
DepositionSep 28, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 10, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc ...entity_src_gen / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _entity_src_gen.pdbx_host_org_cell_line / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Aug 14, 2019Group: Data collection / Database references ...Data collection / Database references / Experimental preparation / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / exptl_crystal_grow
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _exptl_crystal_grow.method / _exptl_crystal_grow.pdbx_details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
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.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_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 / _struct_conn.ptnr2_symmetry
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0May 4, 2022Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_2 / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / 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_seq_id / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_seq_id
Revision 4.0May 11, 2022Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_validate_chiral / struct_asym / 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.auth_comp_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _pdbx_branch_scheme.entity_id / _pdbx_branch_scheme.mon_id / _pdbx_branch_scheme.pdb_mon_id / _pdbx_entity_nonpoly.entity_id / _pdbx_nonpoly_scheme.entity_id / _struct_asym.entity_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_label_comp_id
Revision 4.1Dec 13, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 4.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IG GAMMA-1 CHAIN C REGION
B: IG GAMMA-1 CHAIN C REGION
H: IGM
I: IGM
L: IGM
M: IGM
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,03722
Polymers151,4606
Non-polymers4,57616
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14400 Å2
ΔGint-78.3 kcal/mol
Surface area70770 Å2
MethodPQS
Unit cell
Length a, b, c (Å)241.980, 75.610, 102.400
Angle α, β, γ (deg.)90.00, 91.13, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Antibody , 2 types, 4 molecules HILM

#2: Antibody IGM / FAB HEAVY CHAIN


Mass: 24831.891 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: CD5POSITIVE B CELLS / Cell: B-LYMPHOCYTE / Production host: HOMO SAPIENS (human)
#3: Antibody IGM / FAB LIGHT CHAIN


Mass: 24757.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: CD5POSITIVE B CELLS / Cell: B-LYMPHOCYTE / Production host: HOMO SAPIENS (human)

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein IG GAMMA-1 CHAIN C REGION / IGG1


Mass: 26140.613 Da / Num. of mol.: 2 / Fragment: FC DOMAIN, RESIDUES 99-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO / Production host: CRICETULUS GRISEUS (Chinese hamster) / References: UniProt: P01857
#4: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-beta-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpb1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-2-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE

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Non-polymers , 6 types, 98 molecules

#5: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cd
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#7: Chemical ChemComp-CAC / CACODYLATE ION / dimethylarsinate


Mass: 136.989 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6AsO2
#8: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#9: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 52.1 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6.5
Details: 10% MPEG 5000, 3 MM ZINC ACETATE, 3 MM CDCL2, 100 MM SODIUM CACODYLATE PH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 36545 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.1
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 3.2 / % possible all: 93.8

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1DN2, 2FB4

1dn2

2fb4


Resolution: 3→25 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2877 2563 6.8 %RANDOM
Rwork0.2234 ---
obs0.2234 35995 95.3 %-
Solvent computationBsol: 26.6436 Å2 / ksol: 0.249712 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--37.928 Å20 Å26.472 Å2
2--15.85 Å20 Å2
3---22.078 Å2
Refine analyzeLuzzati coordinate error obs: 0.434 Å / Luzzati d res low obs: 25 Å
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9819 0 292 84 10195
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007422
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.36901
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CARBOHYDRATE.PARAM
X-RAY DIFFRACTION3ION.PARAM
X-RAY DIFFRACTION4WATER.PARAM
X-RAY DIFFRACTION5CACO.PAR

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