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- PDB-4b53: Crystal structure of the isolated IgG4 CH3 domain -

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Basic information

Entry
Database: PDB / ID: 4b53
TitleCrystal structure of the isolated IgG4 CH3 domain
ComponentsIG GAMMA-4 CHAIN C REGION
KeywordsIMMUNE SYSTEM / ANTIBODY / IMMUNOGLOBULIN / FAB ARM EXCHANGE / IGG1
Function / homology
Function and homology information


IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade ...IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / 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
ACETATE ION / DI(HYDROXYETHYL)ETHER / Immunoglobulin heavy constant gamma 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsDavies, A.M. / Rispens, T. / den Bleker, T.H. / McDonnell, J.M. / Gould, H.J. / Aalberse, R.C. / Sutton, B.J.
CitationJournal: Mol.Immunol. / Year: 2012
Title: Crystal Structure of the Human Igg4 C(H)3 Dimer Reveals the Role of Arg409 in the Mechanism of Fab-Arm Exchange.
Authors: Davies, A.M. / Rispens, T. / Den Bleker, T.H. / Mcdonnell, J.M. / Gould, H.J. / Aalberse, R.C. / Sutton, B.J.
History
DepositionAug 2, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 31, 2013Group: Derived calculations / Other
Revision 1.2Sep 4, 2013Group: Atomic model / Derived calculations / Non-polymer description
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc ...exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / struct_conn
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4May 22, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 2.0Mar 4, 2020Group: Derived calculations / Other / Polymer sequence
Category: entity_poly / pdbx_database_status ...entity_poly / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: IG GAMMA-4 CHAIN C REGION
B: IG GAMMA-4 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,04513
Polymers24,1292
Non-polymers91611
Water3,513195
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4230 Å2
ΔGint16 kcal/mol
Surface area10520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.090, 57.090, 138.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-2032-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.0125, 0.9999, -0.0089), (0.9998, -0.0126, -0.0136), (-0.0137, -0.0088, -0.9999)
Vector: -0.1159, 1.0736, 108.4344)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IG GAMMA-4 CHAIN C REGION / HUMAN IGG4


Mass: 12064.380 Da / Num. of mol.: 2 / Fragment: CH3 DOMAIN, RESIDUES 222-327
Source method: isolated from a genetically manipulated source
Details: N TERMINAL GLUTAMINE 342 IS MODIFIED TO PYROGLUTAMATE
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): HEK293F / Production host: HOMO SAPIENS (human) / References: UniProt: P01861

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Non-polymers , 5 types, 206 molecules

#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsGLN342 MODIFIED TO PYROGLUTAMATE IN BOTH CHAINS

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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: 2.34 Å3/Da / Density % sol: 47.38 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: SITTING DROP AT 291K. RESERVOIR OF 100 MICROLITRE 22% PEG 3350 AND 150MM CALCIUM ACETATE. DROP SIZE 100 NANOLITRE PROTEIN AND 100 NANOLITRE RESERVOIR. PROTEIN CONCENTRATION OF 1.5MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.976
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 6, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.8→27.96 Å / Num. obs: 22102 / % possible obs: 99.9 % / Redundancy: 27.1 % / Biso Wilson estimate: 24.8 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 25.8
Reflection shellResolution: 1.8→1.85 Å / Redundancy: 26.3 % / Rmerge(I) obs: 0.76 / Mean I/σ(I) obs: 4.7 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1ADQ

1adq


Resolution: 1.8→27.957 Å / SU ML: 0.24 / σ(F): 1.34 / Phase error: 24.77 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2368 1099 5 %
Rwork0.1826 --
obs0.1851 21991 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.221 Å2 / ksol: 0.347 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-6.9156 Å20 Å20 Å2
2--6.9156 Å20 Å2
3----8.1011 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1640 0 59 195 1894
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061790
X-RAY DIFFRACTIONf_angle_d1.0832413
X-RAY DIFFRACTIONf_dihedral_angle_d15.933680
X-RAY DIFFRACTIONf_chiral_restr0.074255
X-RAY DIFFRACTIONf_plane_restr0.004311
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8001-1.8820.28961340.24612540X-RAY DIFFRACTION99
1.882-1.98120.26861350.21032551X-RAY DIFFRACTION100
1.9812-2.10520.26341330.18742562X-RAY DIFFRACTION100
2.1052-2.26770.25281360.19122571X-RAY DIFFRACTION100
2.2677-2.49580.32561360.1952582X-RAY DIFFRACTION100
2.4958-2.85660.25031370.19482618X-RAY DIFFRACTION100
2.8566-3.59790.22251390.17422649X-RAY DIFFRACTION100
3.5979-27.96020.20181490.16672819X-RAY DIFFRACTION100
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)
13.4298-1.28413.96134.2271-0.63215.235-0.01181.48160.22920.1-0.27080.1358-0.50920.41090.1570.2374-0.0947-0.05720.43590.09270.2446.183517.930336.6604
26.60270.65614.72152.42960.14344.0176-0.597-0.0570.73560.1708-0.2140.0957-1.02880.31940.51320.1766-0.0433-0.0160.29250.03630.169622.024520.240352.0829
35.2610.097-0.16013.02992.94813.08540.1018-0.5342-0.3846-0.15530.02780.23580.42510.3755-0.07660.20210.0255-0.0320.37580.0120.153529.712913.91363.4931
45.7905-0.74893.83190.7015-0.80966.5320.1636-0.18940.0237-0.0621-0.0694-0.07060.4354-0.0694-0.14160.1653-0.0617-0.0230.23670.06030.191720.554714.458651.6098
57.2116-1.65681.97161.55020.33731.4256-0.0239-0.02260.10180.00850.01120.27120.4185-0.49930.06990.1847-0.1179-0.02970.34360.08040.19986.117211.350640.8155
66.5490.99531.14772.8531-0.39215.8114-0.36971.8665-0.1315-0.12630.2364-0.0661.06891.27840.11710.2121-0.00580.01490.26710.010.121121.72427.99243.6739
74.26983.5286-0.8624.52211.50293.18490.06930.29490.1164-0.4905-0.9374-0.97770.49140.10460.75210.29250.08570.0410.40030.11390.329731.05915.883143.141
83.283-1.79361.24773.8593-1.45262.89630.197-0.1547-0.1214-0.30490.00450.07290.3825-0.2558-0.10970.1966-0.0584-0.02370.21440.06460.139413.4868.211450.3304
95.1639-0.29361.07452.87570.9372.3208-0.03510.53360.2236-0.0028-0.03610.315-0.1279-0.13850.07630.1623-0.01810.00180.26080.05830.18249.156115.024148.8489
105.38821.60734.2881.18530.85823.69090.1246-0.2555-0.759-0.12440.1566-0.1420.88970.789-0.67610.16640.0762-0.0190.51520.06840.223230.59149.652355.8276
118.10043.4575-0.41455.70711.05820.40210.1845-0.4359-0.32650.4267-0.369-0.13690.94051.7124-0.06730.17840.068-0.00750.52840.07640.188535.235214.250453.2555
127.3760.11413.66534.3161-1.07474.0331-0.1166-0.15960.1949-0.40980.16360.02720.44650.2824-0.06280.13690.0077-0.00340.35950.01950.169828.502412.989645.4594
135.7236-2.1376.37312.0401-1.66267.70550.42721.3452-0.4153-0.0447-0.52590.34611.1873-0.5477-0.09760.193-0.1334-0.01520.4268-0.03630.168813.068610.61436.7602
141.86890.03892.68472.0345.69176.85180.34051.81630.419-0.39920.8697-1.15440.43190.0181-0.09040.2756-0.10340.00940.620.10360.156116.512312.659532.8877
159.25091.08586.39662.31230.46354.7371-0.37720.5603-0.076-0.27120.583-0.0699-1.05380.1853-0.26360.2447-0.0909-0.00070.30150.02490.143628.589818.506544.6732
162.46910.8423-1.05684.0743-4.98456.12910.2454-0.51410.09961.8665-0.21760.0020.11930.31320.11480.4217-0.076-0.03570.2780.05650.16317.78136.859271.6526
171.4033-0.0888-0.29491.4866-1.4714.3370.09340.105-0.0082-0.2517-0.0507-0.11280.11420.149-0.09750.1677-0.0398-0.00780.240.05350.208319.800520.634458.9835
188.6748-3.9254-4.62889.63671.31094.48890.63991.12861.0518-0.48340.0212-0.4803-1.7894-0.28250.36170.5693-0.01130.04950.46720.2030.324316.01929.617444.9812
191.1188-1.08391.21996.1539-2.66943.7997-0.30850.24930.3028-0.22370.19760.1091-1.058-0.6955-0.04790.39920.0274-0.05640.26820.0940.226612.639324.934553.53
203.31022.0662-0.14693.5394-3.15994.28520.24580.24480.2363-0.0265-0.22480.17440.16820.32180.08070.1787-0.0019-0.01480.1750.03550.166716.879111.423563.3448
218.0892-2.18452.38077.0991-2.1961.46810.07-0.3831-0.256-0.46030.34910.66961.0178-0.7221-0.12390.3136-0.1011-0.00110.24220.03820.21689.91676.064968.0816
225.95472.10131.26467.64460.40380.40350.3075-00.26720.82040.09010.6964-0.6435-0.87520.20120.27760.04120.04560.26250.05980.1897.98522.751964.7196
235.77585.48353.75765.31443.29119.1758-0.0325-1.30250.91150.4466-0.26161.1578-0.82890.2105-0.5360.48910.04520.02530.2766-0.05080.31846.258331.728564.6754
243.5294-1.84530.10033.6311-1.66633.6988-0.0035-0.13150.30980.19370.0771-0.68810.0533-0.6158-0.00540.1679-0.0558-0.02390.25050.0190.17088.084313.872557.7833
252.2231-0.4357-0.33565.4493-0.91861.5239-0.04140.096-0.04010.35740.0117-0.11840.09630.09710.00670.1454-0.01990.00580.1910.01590.127714.82869.516259.3006
263.09071.8194-0.30323.6083-1.89181.1740.15741.15790.6438-0.19860.28061.1973-1.9184-0.53780.10080.78740.20190.05250.2450.22830.29419.674831.833852.9924
275.1405-1.6811-2.75025.81173.43914.59920.23691.26531.1531-0.0042-0.05470.1686-1.8655-1.15520.12680.67340.0980.0830.31360.2460.558715.128436.066955.7256
282.41570.872-0.12754.0473-4.7876.13220.4169-0.00920.21340.37370.12731.2682-0.6531-0.475-0.13780.26990.05160.03040.18590.00580.203911.7323.823365.5223
294.5999-0.61211.97353.65382.01974.35530.0138-0.8840.1181.51050.2081-0.5721.0384-0.7824-0.10350.31920.00790.01470.2443-0.01450.169112.56314.461975.3133
303.43052.3787-1.09599.9113-5.96338.2640.323-0.15810.62120.4865-0.3974-0.3081-0.35530.13570.11420.1964-0.0126-0.0040.13830.01710.341117.197226.516265.0359
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 342:346)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 347:356)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 357:361)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 362:370)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 371:377)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 378:382)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 383:388)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 389:399)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 400:409)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 410:415)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 416:420)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 421:425)
13X-RAY DIFFRACTION13(CHAIN A AND RESID 426:431)
14X-RAY DIFFRACTION14(CHAIN A AND RESID 432:437)
15X-RAY DIFFRACTION15(CHAIN A AND RESID 438:445)
16X-RAY DIFFRACTION16(CHAIN B AND RESID 342:346)
17X-RAY DIFFRACTION17(CHAIN B AND RESID 347:354)
18X-RAY DIFFRACTION18(CHAIN B AND RESID 355:361)
19X-RAY DIFFRACTION19(CHAIN B AND RESID 362:367)
20X-RAY DIFFRACTION20(CHAIN B AND RESID 368:372)
21X-RAY DIFFRACTION21(CHAIN B AND RESID 373:377)
22X-RAY DIFFRACTION22(CHAIN B AND RESID 378:382)
23X-RAY DIFFRACTION23(CHAIN B AND RESID 383:388)
24X-RAY DIFFRACTION24(CHAIN B AND RESID 389:399)
25X-RAY DIFFRACTION25(CHAIN B AND RESID 400:409)
26X-RAY DIFFRACTION26(CHAIN B AND RESID 410:416)
27X-RAY DIFFRACTION27(CHAIN B AND RESID 417:421)
28X-RAY DIFFRACTION28(CHAIN B AND RESID 422:428)
29X-RAY DIFFRACTION29(CHAIN B AND RESID 429:436)
30X-RAY DIFFRACTION30(CHAIN B AND RESID 437:443)

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