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- PDB-2wah: Crystal Structure of an IgG1 Fc Glycoform (Man9GlcNAc2) -

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Basic information

Entry
Database: PDB / ID: 2wah
TitleCrystal Structure of an IgG1 Fc Glycoform (Man9GlcNAc2)
ComponentsIG GAMMA-1 CHAIN C REGION
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN C REGION / ANTIBODY ENGINEERING / IMMUNOGLOBULIN DOMAIN / SECRETED / ANTIBODY / KIFUNENSINE / GLYCOPROTEIN / OLIGOMANNOSE / GLYCOSYLATION
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
Immunoglobulin heavy constant gamma 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.51 Å
AuthorsCrispin, M. / Bowden, T.A. / Coles, C.H. / Harlos, K. / Aricescu, A.R. / Harvey, D.J. / Stuart, D.I. / Jones, E.Y.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Carbohydrate and Domain Architecture of an Immature Antibody Glycoform Exhibiting Enhanced Effector Functions
Authors: Crispin, M. / Bowden, T.A. / Coles, C.H. / Harlos, K. / Aricescu, A.R. / Harvey, D.J. / Stuart, D.I. / Jones, E.Y.
History
DepositionFeb 6, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_tissue
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / 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_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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.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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5494
Polymers47,4042
Non-polymers2,1462
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-9.9 kcal/mol
Surface area28540 Å2
MethodPQS
Unit cell
Length a, b, c (Å)49.391, 74.977, 149.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 23701.766 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN GAMMA, FC, RESIDUES 120-328 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HOMOGENOUS (MAN)9(NAG)2 GLYCOFORM OF HUMAN IGG1 FC.
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PHLSEC / Cell line (production host): HEK293T / Production host: Homo sapiens (human) / References: UniProt: P01857
#2: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 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)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 276 TO ALA ENGINEERED RESIDUE IN CHAIN B, THR 276 TO ALA
Has protein modificationY
Sequence detailsT393A MUTATION AROSE DURING CLONING

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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: 2.9 Å3/Da / Density % sol: 58 % / Description: NONE
Crystal growpH: 6 / Details: 20% PEG 6000, 0.1 M MES PH 6.0

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Data collection

DiffractionMean temperature: 77.2 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97626
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 8, 2007 / Details: MIRRORS
RadiationMonochromator: SINGLE SILICON (111) MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 2.51→29.87 Å / Num. obs: 19180 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.3
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.84 / Mean I/σ(I) obs: 2.5 / % possible all: 93.1

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Processing

Software
NameVersionClassification
REFMAC5.5.0047refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DTQ

2dtq
PDB Unreleased entry


Resolution: 2.51→29.87 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.895 / SU B: 21.412 / SU ML: 0.22 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.53 / ESU R Free: 0.306 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.268 988 5.2 %RANDOM
Rwork0.216 ---
obs0.219 18192 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.57 Å2
Baniso -1Baniso -2Baniso -3
1--1.64 Å20 Å20 Å2
2--0.04 Å20 Å2
3---1.61 Å2
Refinement stepCycle: LAST / Resolution: 2.51→29.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3327 0 144 94 3565
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0223580
X-RAY DIFFRACTIONr_bond_other_d0.0010.022429
X-RAY DIFFRACTIONr_angle_refined_deg1.3212.0074898
X-RAY DIFFRACTIONr_angle_other_deg0.8223.0035940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4265414
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.31625152
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.30315578
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9951512
X-RAY DIFFRACTIONr_chiral_restr0.0750.2571
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213840
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02638
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4071.52098
X-RAY DIFFRACTIONr_mcbond_other0.0881.5813
X-RAY DIFFRACTIONr_mcangle_it0.77423447
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.34431482
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.2484.51451
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.51→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 68 -
Rwork0.276 1230 -
obs--91.93 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.12031.8272-1.32823.6402-0.42335.2689-0.06221.17070.3155-0.57090.2729-0.0659-0.4581-0.1698-0.21070.2122-0.0040.00570.37420.10260.072-15.366-17.56913.608
25.9155-0.46241.82432.59060.43083.2045-0.1499-0.27690.2290.33230.1088-0.0018-0.1120.01660.04110.05160.0134-0.0020.0186-0.01130.0094-5.394-28.53742.574
33.90730.93782.83763.19081.82847.465-0.1821.4217-0.894-0.5771-0.22930.42410.27990.1270.41130.2175-0.03960.01650.724-0.56350.479316.037-49.14111.078
46.31550.0525-1.36864.2204-1.35733.1553-0.1297-0.2805-0.4110.15250.0975-0.0730.1271-0.28820.03210.0173-0.00990.00110.05620.02690.03055.196-41.39441.666
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 338
2X-RAY DIFFRACTION2A339 - 444
3X-RAY DIFFRACTION3B237 - 338
4X-RAY DIFFRACTION4B339 - 444

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