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- PDB-4acp: Deactivation of human IgG1 Fc by endoglycosidase treatment -

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Basic information

Entry
Database: PDB / ID: 4acp
TitleDeactivation of human IgG1 Fc by endoglycosidase treatment
ComponentsIG GAMMA-1 CHAIN C REGION
KeywordsIMMUNE SYSTEM / IGG / ANTIBODY / KIFUNENSINE
Function / homology
Function and homology information


complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis ...complement-dependent cytotoxicity / antibody-dependent cellular cytotoxicity / Fc-gamma receptor I complex binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / FCGR activation / Role of phospholipids in phagocytosis / complement activation, classical pathway / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / B cell receptor signaling pathway / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / 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: 2.49 Å
AuthorsRaman, K. / Bowden, T.A. / Krishna, B.A. / Dwek, R.A. / Crispin, M. / Scanlan, C.N.
CitationJournal: J.Mol.Biol. / Year: 2012
Title: Selective Deactivation of Serum Igg: A General Strategy for the Enhancement of Monoclonal Antibody Receptor Interactions.
Authors: Baruah, K. / Bowden, T.A. / Krishna, B.A. / A Dwek, R. / Crispin, M. / Scanlan, C.N.
History
DepositionDec 16, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 25, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2012Group: Other
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Dec 20, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)54,2523
Polymers54,0312
Non-polymers2211
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-8.5 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.290, 110.857, 77.508
Angle α, β, γ (deg.)90.00, 107.92, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2004-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 5 / Auth seq-ID: 341 - 444 / Label seq-ID: 126 - 229

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.862632, -0.499578, -0.079291), (-0.497106, 0.808281, 0.315543), (-0.093549, 0.311613, -0.945593)-39.07106, -17.14447, 37.04609

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Components

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


Mass: 27015.525 Da / Num. of mol.: 2 / Fragment: IMMUNOGLOBULIN GAMMA, FC, RESIDUES 101-329
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line: 293T / Plasmid: PHLSEC / Cell line (production host): 293T / Production host: HOMO SAPIENS (human) / References: UniProt: P01857
#2: 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.: 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
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
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: 3.15 Å3/Da / Density % sol: 60 % / Description: NONE
Crystal growpH: 4
Details: 25% W/V POLYETHYLENE GLYCOL 1500, 0.1 M SPG SYSTEM BUFFER PH 4

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 14, 2010 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→34.3 Å / Num. obs: 19399 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 19.5
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2DTQ

2dtq
PDB Unreleased entry


Resolution: 2.49→36.87 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.938 / SU B: 20.809 / SU ML: 0.212 / Cross valid method: THROUGHOUT / ESU R: 0.392 / ESU R Free: 0.252 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23424 980 5.1 %RANDOM
Rwork0.19485 ---
obs0.1968 18408 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.735 Å2
Baniso -1Baniso -2Baniso -3
1-2.49 Å20 Å24.72 Å2
2---2.81 Å20 Å2
3---3.22 Å2
Refinement stepCycle: LAST / Resolution: 2.49→36.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3252 0 14 25 3291
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.023358
X-RAY DIFFRACTIONr_bond_other_d0.0010.022301
X-RAY DIFFRACTIONr_angle_refined_deg1.2381.9594569
X-RAY DIFFRACTIONr_angle_other_deg0.7783.0035638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.185401
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28324.932148
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83215570
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.9221512
X-RAY DIFFRACTIONr_chiral_restr0.0690.2506
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213633
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02631
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A611medium positional0.160.5
2B611medium positional0.160.5
1A795loose positional0.555
2B795loose positional0.555
1A611medium thermal3.342
2B611medium thermal3.342
1A795loose thermal3.9410
2B795loose thermal3.9410
LS refinement shellResolution: 2.494→2.559 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.36 58 -
Rwork0.307 1290 -
obs--97.68 %
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)
12.5142-1.6642-0.61426.25-0.24435.63270.0265-0.31720.81840.6076-0.2913-0.7191-0.12340.10390.26480.26750.07160.20220.29550.0090.8726-33.343-4.64932.033
25.0048-4.0390.01257.0747-0.71743.13-0.2738-0.36020.220.75220.5484-0.0658-0.562-0.4074-0.27460.19380.0932-0.00450.1010.07040.2017-11.4798.46810.054
35.4410.4342-0.37573.3121-0.37843.7637-0.0443-0.4790.02190.5256-0.07070.52180.3356-0.24650.11490.2529-0.04910.05910.0668-0.00970.2506-19.012-28.82722.103
44.29512.35250.21434.85140.72122.1727-0.28660.10580.05330.03120.17510.19030.0821-0.01470.11150.14050.0202-0.09950.01970.0060.1813-10.11-24.1218.908
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A236 - 339
2X-RAY DIFFRACTION2B236 - 339
3X-RAY DIFFRACTION3A340 - 444
4X-RAY DIFFRACTION4B340 - 444

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