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- PDB-4x4m: Structure of FcgammaRI in complex with Fc reveals the importance ... -

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Basic information

Entry
Database: PDB / ID: 4x4m
TitleStructure of FcgammaRI in complex with Fc reveals the importance of glycan recognition for high affinity IgG binding
Components
  • High affinity immunoglobulin gamma Fc receptor I
  • Ig gamma-1 chain C region
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


high-affinity IgG receptor activity / positive regulation of type III hypersensitivity / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / Cross-presentation of soluble exogenous antigens (endosomes) / Classical antibody-mediated complement activation ...high-affinity IgG receptor activity / positive regulation of type III hypersensitivity / phagocytosis, recognition / positive regulation of type IIa hypersensitivity / complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / IgG binding / Fc-gamma receptor I complex binding / Cross-presentation of soluble exogenous antigens (endosomes) / Classical antibody-mediated complement activation / phagocytosis, engulfment / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / antigen processing and presentation of exogenous peptide antigen via MHC class I / FCGR activation / regulation of immune response / Role of phospholipids in phagocytosis / positive regulation of protein tyrosine kinase activity / positive regulation of phagocytosis / complement activation, classical pathway / antigen binding / receptor-mediated endocytosis / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / clathrin-coated endocytic vesicle membrane / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / Interferon gamma signaling / transmembrane signaling receptor activity / antibacterial humoral response / early endosome membrane / blood microparticle / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / cell surface receptor signaling pathway / defense response to bacterium / immune response / external side of plasma membrane / innate immune response / signal transduction / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin subtype / Immunoglobulin / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
beta-L-fucopyranose / Immunoglobulin heavy constant gamma 1 / High affinity immunoglobulin gamma Fc receptor I
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.485 Å
AuthorsLu, J. / Sun, P.D.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structure of Fc gamma RI in complex with Fc reveals the importance of glycan recognition for high-affinity IgG binding.
Authors: Lu, J. / Chu, J. / Zou, Z. / Hamacher, N.B. / Rixon, M.W. / Sun, P.D.
History
DepositionDec 3, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_gen / 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_struct_assembly_gen / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_comp_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_unobs_or_zero_occ_atoms.label_comp_id / _pdbx_unobs_or_zero_occ_atoms.label_seq_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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.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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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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
C: Ig gamma-1 chain C region
D: Ig gamma-1 chain C region
E: High affinity immunoglobulin gamma Fc receptor I
F: High affinity immunoglobulin gamma Fc receptor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,34713
Polymers160,8246
Non-polymers6,5237
Water0
1
A: Ig gamma-1 chain C region
B: Ig gamma-1 chain C region
E: High affinity immunoglobulin gamma Fc receptor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,3395
Polymers80,4123
Non-polymers2,9272
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Ig gamma-1 chain C region
D: Ig gamma-1 chain C region
F: High affinity immunoglobulin gamma Fc receptor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0088
Polymers80,4123
Non-polymers3,5965
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)59.921, 67.991, 125.028
Angle α, β, γ (deg.)89.86, 112.25, 89.96
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection details
111chain 'E' and (resseq 21:46 or resseq 53:58 or resseq...
211chain 'F' and (resseq 21:46 or resseq 53:58 or resseq...
112chain 'B' and (resseq 231:444 ) and (not element H)
212chain 'D' and (resseq 231:444 ) and (not element H)
113chain 'A' and (resseq 232:443 ) and (not element H)
213chain 'C' and (resseq 232:443 ) and (not element H)

NCS ensembles :
ID
1
2
3

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Components

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Protein , 2 types, 6 molecules ABCDEF

#1: Protein
Ig gamma-1 chain C region


Mass: 24698.955 Da / Num. of mol.: 4 / Fragment: CH2 and CH3 regions, residues 112-330
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGHG1 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01857
#2: Protein High affinity immunoglobulin gamma Fc receptor I / IgG Fc receptor I / Fc-gamma RI / FcRI / Fc-gamma RIA / FcgammaRIa


Mass: 31014.074 Da / Num. of mol.: 2 / Fragment: Extracellular residues 21-289
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FCGR1A, FCG1, FCGR1, IGFR1 / Production host: Escherichia coli (E. coli) / References: UniProt: P12314

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Sugars , 6 types, 7 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]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: 1463.349 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_a6-h1_b4-c1_c3-d1_c6-f1_d2-e1_f2-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#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)-alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]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]/1-1-2-3-1-3-1-4-5/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)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}}LINUCSPDB-CARE
#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1114.016 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-2-3-1-3-1/a4-b1_b3-c1_b6-e1_c2-d1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#6: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose


Type: oligosaccharide / Mass: 471.411 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2/a3-b2WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-Galp]{[(3+2)][a-D-Neup5Ac]{}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
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
#8: Sugar ChemComp-FUL / beta-L-fucopyranose / 6-DEOXY-BETA-L-GALACTOSE / Fucose


Type: L-saccharide, beta linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-L-fucopyranoseCOMMON NAMEGMML 1.0
b-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.04 % / Description: plates
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / Details: PEG8000, 10mM Hepes(pH7.5), 50mM Lithium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 8, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.485→50 Å / Num. obs: 20950 / % possible obs: 91.5 % / Observed criterion σ(I): 1 / Redundancy: 5 % / Biso Wilson estimate: 127 Å2 / Rmerge(I) obs: 0.135 / Net I/σ(I): 22.1
Reflection shellResolution: 3.485→3.56 Å / Redundancy: 1.5 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 1 / % possible all: 68.8

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
SCALAdata scaling
PHASERphasing
RefinementResolution: 3.485→40.665 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 41.26 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2957 1084 5.18 %
Rwork0.2453 --
obs0.2493 20943 89.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.485→40.665 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10930 0 438 0 11368
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00611703
X-RAY DIFFRACTIONf_angle_d1.71715969
X-RAY DIFFRACTIONf_dihedral_angle_d15.4994150
X-RAY DIFFRACTIONf_chiral_restr0.0631868
X-RAY DIFFRACTIONf_plane_restr0.0071977
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11E1898X-RAY DIFFRACTIONPOSITIONAL
12F1898X-RAY DIFFRACTIONPOSITIONAL0.072
21B1705X-RAY DIFFRACTIONPOSITIONAL
22D1705X-RAY DIFFRACTIONPOSITIONAL0.015
31A1694X-RAY DIFFRACTIONPOSITIONAL
32C1694X-RAY DIFFRACTIONPOSITIONAL0.018
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.4898-3.67350.34561030.3171968X-RAY DIFFRACTION60
3.6735-3.90320.33551300.29552492X-RAY DIFFRACTION75
3.9032-4.20380.32281760.29693001X-RAY DIFFRACTION90
4.2038-4.62540.26611530.26643167X-RAY DIFFRACTION95
4.6254-5.29150.30641650.25183099X-RAY DIFFRACTION94
5.2915-6.65440.37261580.26023107X-RAY DIFFRACTION94
6.6544-29.78630.25031510.20583056X-RAY DIFFRACTION92

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