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- PDB-4d2n: Crystal structure of deglycosylated serum-derived human IgG4 Fc -

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Basic information

Entry
Database: PDB / ID: 4d2n
TitleCrystal structure of deglycosylated serum-derived human IgG4 Fc
ComponentsIG GAMMA-4 CHAIN C REGION
KeywordsIMMUNE SYSTEM / IGG / IMMUNOGLOBULIN / IGG1
Function / homology
Function and homology information


IgG immunoglobulin complex / 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 ...IgG immunoglobulin complex / 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 4
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsDavies, A.M. / Jefferis, R. / Sutton, B.J.
CitationJournal: Mol.Immunol. / Year: 2014
Title: Crystal Structure of Deglycosylated Human Igg4-Fc
Authors: Davies, A.M. / Jefferis, R. / Sutton, B.J.
History
DepositionMay 12, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 22, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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
C: IG GAMMA-4 CHAIN C REGION
D: IG GAMMA-4 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,8875
Polymers101,7954
Non-polymers921
Water21612
1
C: IG GAMMA-4 CHAIN C REGION
D: IG GAMMA-4 CHAIN C REGION


Theoretical massNumber of molelcules
Total (without water)50,8972
Polymers50,8972
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-12.4 kcal/mol
Surface area20970 Å2
MethodPISA
2
A: IG GAMMA-4 CHAIN C REGION
B: IG GAMMA-4 CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,9893
Polymers50,8972
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2350 Å2
ΔGint-10.4 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)196.945, 196.945, 96.956
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number177
Space group name H-MP622
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.8582, 0.5133, 0.0078), (0.5134, 0.8581, 0.0085), (-0.0024, 0.0113, -0.9999)-0.5206, 0.1066, 49.042
2given(-0.282, -0.2012, 0.9381), (-0.2381, -0.9325, -0.2716), (0.9294, -0.2999, 0.2151)-60.314, -129.0635, 15.9454
3given(0.1108, -0.2853, -0.952), (-0.3082, -0.9205, 0.24), (-0.9448, 0.2668, -0.1899)-13.0665, -141.838, 28.8137

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Components

#1: Protein
IG GAMMA-4 CHAIN C REGION


Mass: 25448.658 Da / Num. of mol.: 4 / Fragment: FC FRAGMENT, RESIDUES 102-327 / Mutation: YES / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P01861
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsASN297 CONVERTED TO ASP THROUGH ACTION OF PNGASE F ENZYME

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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: 2.7 Å3/Da / Density % sol: 54.7 %
Description: RPIM VALUES OF 0.04 OVERALL AND 0.61 OUTER SHELL
Crystal growTemperature: 291 K / pH: 7
Details: CRYSTALS WERE GROWN AT 291K USING A RESERVOIR OF 100MM BIS-TRIS PROPANE PH7.5, 20% PEG 3350 AND 200MM SODIUM CITRATE, AND A PROTEIN CONCENTRATION OF 6MG/ML.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Feb 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.7→53.7 Å / Num. obs: 30902 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 20 % / Biso Wilson estimate: 68.57 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 16.9
Reflection shellResolution: 2.7→2.83 Å / Redundancy: 20 % / Mean I/σ(I) obs: 1.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C54

4c54


Resolution: 2.7→53.682 Å / SU ML: 0.38 / σ(F): 1.91 / Phase error: 27.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2544 1545 5 %
Rwork0.2045 --
obs0.207 30889 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→53.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6310 0 6 12 6328
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026497
X-RAY DIFFRACTIONf_angle_d0.6038885
X-RAY DIFFRACTIONf_dihedral_angle_d11.432290
X-RAY DIFFRACTIONf_chiral_restr0.0241013
X-RAY DIFFRACTIONf_plane_restr0.0031145
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.78720.37761380.33682614X-RAY DIFFRACTION100
2.7872-2.88680.32911370.30782606X-RAY DIFFRACTION100
2.8868-3.00240.32031370.29062615X-RAY DIFFRACTION100
3.0024-3.1390.30771400.26652645X-RAY DIFFRACTION100
3.139-3.30450.28231370.25052605X-RAY DIFFRACTION100
3.3045-3.51150.30361400.21972652X-RAY DIFFRACTION100
3.5115-3.78250.24491400.20872661X-RAY DIFFRACTION100
3.7825-4.1630.29171390.18942645X-RAY DIFFRACTION100
4.163-4.76510.19061420.15232691X-RAY DIFFRACTION100
4.7651-6.00230.21331430.16282722X-RAY DIFFRACTION100
6.0023-53.69290.24191520.20472888X-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)
11.27940.77360.67021.08720.1192.0813-0.0310.3539-0.6051-0.1702-0.0349-0.36870.24470.0387-0.25890.6293-0.14490.0510.5126-0.09950.6461-37.9964-60.709622.504
20.9584-0.08110.16380.17010.27491.14230.011-0.02750.2318-0.05180.0472-0.0492-0.1448-0.06110.00010.35350.00020.08430.31030.01940.3791-18.7776-34.7722.7682
30.59970.01660.55130.7276-0.39631.368-0.1105-0.1912-0.48760.53-0.05240.1557-0.16-0.08490.14980.8171-0.12030.15470.4615-0.05590.70980.2464-71.855928.2262
41.1583-1.0953-0.40970.75660.05671.09170.01040.02640.07930.0663-0.03350.08070.1414-0.0186-0.00030.3264-0.07480.05390.2972-0.08660.3234-1.1621-47.622124.9359
50.39990.0951-0.01960.3768-0.03570.01340.3028-0.12440.32210.25010.50320.21360.1848-0.63750.05530.984-0.37930.02870.7494-0.11080.53-19.6124-76.49555.4183
60.0359-0.08980.06420.0588-0.03320.0098-0.41880.5894-0.40360.38390.7629-0.5269-1.07150.2446-0.00011.1269-0.13560.20030.7445-0.1050.9837-15.5198-61.26893.1598
70.31820.4136-0.09420.7122-0.47460.46760.24420.0057-0.1915-0.3992-0.0085-0.088-0.602-0.6306-0.0810.9469-0.03110.18881.01360.03230.9479-20.178-64.31022.7932
8-0.04760.0231-0.03160.1269-0.11940.0604-0.06250.0625-0.1497-0.11940.0568-1.0367-0.0707-0.2438-0.00010.8155-0.27110.15860.7981-0.29210.9631-11.6562-73.05363.7993
90.68160.3505-0.06681.07250.16670.7867-0.41010.3005-0.4958-0.34330.4044-0.01260.1561-0.061-0.02440.7752-0.30350.00210.5089-0.05310.6685-27.8733-98.440514.8434
100.43410.33620.73380.11020.27580.8303-0.0752-0.05440.0249-0.40240.24810.00720.07290.0975-0.00010.8774-0.23570.01870.5698-0.01720.5615-20.7473-70.194542.8245
110.2236-0.33990.22270.8053-0.43090.26410.3825-0.1701-0.1903-0.1976-0.2389-0.2151-0.08820.3931-0.14870.8648-0.10490.12670.8422-0.31970.7665-15.4234-66.176945.4379
121.0074-0.68730.67620.70090.13140.81820.0446-0.11990.0820.1592-0.4896-0.305-0.0433-0.4817-0.00010.7368-0.21990.03520.72240.00780.5853-29.4913-71.74442.8667
131.12040.48190.04310.80690.23371.26020.2268-0.1501-0.54040.5316-0.38090.13660.23280.08-0.00730.7645-0.2153-0.05590.43290.06950.6024-27.0788-99.926231.9594
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 236 THROUGH 336 )
2X-RAY DIFFRACTION2CHAIN A AND (RESID 337 THROUGH 444 )
3X-RAY DIFFRACTION3CHAIN B AND (RESID 238 THROUGH 299 )
4X-RAY DIFFRACTION4CHAIN B AND (RESID 300 THROUGH 443 )
5X-RAY DIFFRACTION5CHAIN C AND (RESID 237 THROUGH 264 )
6X-RAY DIFFRACTION6CHAIN C AND (RESID 265 THROUGH 279 )
7X-RAY DIFFRACTION7CHAIN C AND (RESID 280 THROUGH 301 )
8X-RAY DIFFRACTION8CHAIN C AND (RESID 302 THROUGH 337 )
9X-RAY DIFFRACTION9CHAIN C AND (RESID 338 THROUGH 443 )
10X-RAY DIFFRACTION10CHAIN D AND (RESID 235 THROUGH 279 )
11X-RAY DIFFRACTION11CHAIN D AND (RESID 280 THROUGH 301 )
12X-RAY DIFFRACTION12CHAIN D AND (RESID 302 THROUGH 346 )
13X-RAY DIFFRACTION13CHAIN D AND (RESID 347 THROUGH 443 )

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