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- PDB-2vuo: Crystal structure of the rabbit IgG Fc fragment -

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Basic information

Entry
Database: PDB / ID: 2vuo
TitleCrystal structure of the rabbit IgG Fc fragment
ComponentsIG GAMMA CHAIN C REGION
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN C REGION / IGG / RABBIT / FC FRAGMENT / GLYCOSYLATION / IMMUNOGLOBULINS / IMMUNOGLOBULIN DOMAIN
Function / homology
Function and homology information


immunoglobulin complex, circulating / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / antibacterial humoral response / blood microparticle / extracellular exosome
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
AZIDE ION / FORMIC ACID / Ig gamma chain C region
Similarity search - Component
Biological speciesORYCTOLAGUS CUNICULUS (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsGirardi, E. / Holdom, M.D. / Davies, A.M. / Sutton, B.J. / Beavil, A.J.
CitationJournal: Biochem.J. / Year: 2009
Title: The Crystal Structure of Rabbit Igg-Fc.
Authors: Girardi, E. / Holdom, M.D. / Davies, A.M. / Sutton, B.J. / Beavil, A.J.
History
DepositionMay 27, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Derived calculations ...Data collection / Derived calculations / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / 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 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _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 / Derived calculations / 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_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
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 CHAIN C REGION
B: IG GAMMA CHAIN C REGION
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,99416
Polymers49,5102
Non-polymers3,48414
Water7,170398
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2540 Å2
ΔGint-18.3 kcal/mol
Surface area27730 Å2
MethodPQS
Unit cell
Length a, b, c (Å)58.662, 71.211, 69.036
Angle α, β, γ (deg.)90.00, 104.78, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein IG GAMMA CHAIN C REGION / IMMUNOGLOBULIN GAMMA HEAVY CHAIN CONSTANT REGION


Mass: 24755.117 Da / Num. of mol.: 2 / Fragment: FC FRAGMENT, RESIDUES 229-447 / Source method: isolated from a natural source
Details: FC FRAGMENT, COMMERCIALLY AVAILABLE RABBIT IGG PURIFIED FROM SERUM (SIGMA-ALDRICH, UK)
Source: (natural) ORYCTOLAGUS CUNICULUS (rabbit) / References: UniProt: P01870

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Sugars , 2 types, 2 molecules

#2: 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)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1479.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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][a2112h-1b_1-5]/1-1-2-3-1-3-1-4/a4-b1_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]{}}}}}}}LINUCSPDB-CARE
#3: 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)-[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: 1276.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-1-2-3-3-1-4/a4-b1_b4-c1_c3-d1_c6-e1_e2-f1_f4-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 410 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: N3
#6: Chemical
ChemComp-FMT / FORMIC ACID / Formic acid


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 398 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsSEQUENCE BELONGS TO ALLOTYPE E14 WHERE THR IS FOUND AT POSITION 309. ACCORDING TO DENSITY, AN ALA ...SEQUENCE BELONGS TO ALLOTYPE E14 WHERE THR IS FOUND AT POSITION 309. ACCORDING TO DENSITY, AN ALA WAS MODELLED AT POSITION 309, CORRESPONDING TO THE E15 ALLOTYPE. MOREOVER, A SER WAS MODELLED AT POSITION 408 ACCORDING TO DENSITY AND IN AGREEMENT WITH SEQUENCE VARIABILITY DESCRIBED AT THIS POSITION

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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: 2.53 Å3/Da / Density % sol: 51.1 % / Description: NONE
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.7
Details: HANGING DROP, VAPOUR DIFFUSION AT 291K. 2M SODIUM FORMATE, 0.1M SODIUM ACETATE, PH 4.7, PROTEIN CONCENTRATION 2MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.976
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 13, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.95→56.7 Å / Num. obs: 40194 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 21.43 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 17.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 3.6 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H3T

1h3t


Resolution: 1.95→56.721 Å / SU ML: 0.2 / Phase error: 13.53 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.204 2013 5.01 %
Rwork0.1693 --
obs0.1676 40177 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 54.381 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 26.63 Å2
Baniso -1Baniso -2Baniso -3
1-0.9483 Å20 Å20.9031 Å2
2--2.227 Å2-0 Å2
3----3.1752 Å2
Refinement stepCycle: LAST / Resolution: 1.95→56.721 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3344 0 234 398 3976
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043825
X-RAY DIFFRACTIONf_angle_d0.9385234
X-RAY DIFFRACTIONf_dihedral_angle_d26.3891488
X-RAY DIFFRACTIONf_chiral_restr0.059612
X-RAY DIFFRACTIONf_plane_restr0.004654
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-1.97220.17313340.1731334X-RAY DIFFRACTION100
1.9722-1.99540.157413250.15741325X-RAY DIFFRACTION100
1.9954-2.01970.164313440.16431344X-RAY DIFFRACTION100
2.0197-2.04530.158613200.15861320X-RAY DIFFRACTION100
2.0453-2.07220.157613310.15761331X-RAY DIFFRACTION100
2.0722-2.10060.161613460.16161346X-RAY DIFFRACTION100
2.1006-2.13060.171112990.17111299X-RAY DIFFRACTION100
2.1306-2.16240.147913690.14791369X-RAY DIFFRACTION99.93
2.1624-2.19620.155113110.15511311X-RAY DIFFRACTION100
2.1962-2.23220.15213510.1521351X-RAY DIFFRACTION100
2.2322-2.27070.151813070.15181307X-RAY DIFFRACTION100
2.2707-2.3120.156213730.15621373X-RAY DIFFRACTION99.93
2.312-2.35640.164513430.16451343X-RAY DIFFRACTION100
2.3564-2.40450.162312940.16231294X-RAY DIFFRACTION100
2.4045-2.45680.162713570.16271357X-RAY DIFFRACTION100
2.4568-2.5140.169213050.16921305X-RAY DIFFRACTION100
2.514-2.57680.168313450.16831345X-RAY DIFFRACTION100
2.5768-2.64650.173313550.17331355X-RAY DIFFRACTION100
2.6465-2.72440.179413270.17941327X-RAY DIFFRACTION100
2.7244-2.81230.18913370.1891337X-RAY DIFFRACTION100
2.8123-2.91280.182313530.18231353X-RAY DIFFRACTION100
2.9128-3.02950.172613290.17261329X-RAY DIFFRACTION100
3.0295-3.16730.169413380.16941338X-RAY DIFFRACTION100
3.1673-3.33430.164113340.16411334X-RAY DIFFRACTION100
3.3343-3.54320.163913550.16391355X-RAY DIFFRACTION100
3.5432-3.81670.150313370.15031337X-RAY DIFFRACTION100
3.8167-4.20070.138813580.13881358X-RAY DIFFRACTION100
4.2007-4.80820.142213610.14221361X-RAY DIFFRACTION100
4.8082-6.05680.149113550.14911355X-RAY DIFFRACTION100
6.0568-56.7450.190113840.19011384X-RAY DIFFRACTION98.86
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)
18.9994-2.64015.76770.26430.1041-0.3260.25431.14060.8025-0.0267-0.8032-0.0710.58920.56040.25530.38090.18120.20370.65460.29650.4832-31.85512.951458.6006
21.5138-0.3054-0.50381.26280.0253-0.4396-0.056-0.2766-0.08580.199-0.00650.0089-0.02240.07360.02120.12770.01110.00250.1638-0.0170.1105-18.85115.729242.2418
37.770.3016.4609-1.7525-1.61624.8963-0.6097-0.33930.86510.1984-0.07810.1901-0.7834-0.15010.65530.31860.0376-0.09550.2681-0.13050.3642-10.779924.841844.6196
41.2967-3.3061-1.33211.37012.15395.0643-0.0816-0.13850.36080.2356-0.0131-0.36270.24950.42630.02590.15340.0310.0490.25280.0090.2156-25.652521.761646.2954
50.22910.1294-0.65080.33690.18611.2215-0.0004-0.1865-0.14860.0831-0.0143-0.0719-0.07730.24220.01460.05840.0248-0.00970.1190.01060.0893-17.734315.83941.1434
63.0504-0.5648-2.70450.20360.62065.72-0.0709-0.6788-0.10620.13440.2007-0.06950.07221.1836-0.05630.14610.0479-0.01860.2007-0.01050.1395-11.74129.886543.1096
70.10420.0298-0.05811.196-0.54911.7467-0.03010.05930.0532-0.130.15680.00580.14880.025-0.06310.0507-0.0196-0.03240.05530.01170.0498-23.00324.808410.7837
82.1947-1.34732.71966.4-4.48074.622-0.25680.74990.57380.18820.30440.1121-0.5760.16630.03160.1562-0.0326-0.06870.20690.14450.2477-28.755217.03319.3804
91.0240.43140.4591.25750.06131.1067-0.0718-0.05620.1316-0.07460.16530.1078-0.0313-0.1183-0.06970.0458-0.0057-0.01870.07710.02950.0831-25.63317.3512.4102
103.54140.89623.06980.38220.94913.1427-0.10380.50770.2726-0.08810.0880.07090.07580.48520.00440.1274-0.0244-0.03610.15240.04510.1136-17.274714.56979.5156
11-0.57250.83243.55650.3328-2.8564-0.482-0.1195-0.47860.34660.14320.3888-0.1466-0.2711-0.1327-0.07970.1780.04690.01880.3173-0.14790.2362-27.4835-8.665350.8089
120.6431-0.23280.26050.7597-0.32814.1810.0814-0.1350.0824-0.0850.0751-0.12010.34210.2421-0.1160.09570.02310.02140.1176-0.01390.1177-26.8082-19.191234.0336
135.0388-1.42373.98330.869-1.19734.1932-0.0555-0.7179-0.40370.12480.30180.0937-0.1972-0.4913-0.18520.10710.00240.02740.26070.0240.0981-33.6402-22.329546.129
141.8932-0.6384-0.60090.88910.27620.556-0.1492-0.71520.2998-0.09570.18240.2323-0.0188-0.248-0.04390.0655-0.0115-0.04820.25140.00590.1954-18.8103-20.678345.1979
151.1754-0.09080.82050.8293-0.61590.65660.072-0.2980.0728-0.07970.06660.1169-0.0005-0.1961-0.08880.0655-0.00310.0180.1499-0.00250.0898-34.1262-20.407236.06
161.8696-0.28981.82830.4167-0.25541.029-0.0868-0.49410.11540.13710.15460.0053-0.1283-0.593-0.03090.09130.04080.01690.1764-0.02090.0897-35.5208-13.416541.0276
170.96610.4434-0.08740.52640.61770.98670.02230.14170.0716-0.1260.13040.008-0.30380.1896-0.12680.1351-0.04550.02240.13440.01740.0848-19.8607-3.42425.2824
181.8384-0.08140.19820.6150.41330.9351-0.0890.0448-0.0390.10410.04640.02370.07390.06690.02920.05910.0027-0.01150.05940.01910.0611-26.6182-8.196915.6829
190.1562-0.2758-0.44920.26910.47271.77920.029-0.00330.0022-0.00210.0899-0.07310.06460.3544-0.09180.0799-0.00860.01340.1992-0.0370.0851-12.7229-9.97852.6141
201.12290.43570.04570.74060.74360.1232-0.17540.249-0.1793-0.01160.1678-0.01380.0073-0.00260.0580.1093-0.02470.01270.083-0.00590.0739-28.4187-15.33818.7063
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 230:235)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 236:281)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 282:287)
4X-RAY DIFFRACTION4CHAIN A AND (RESID 288:293)
5X-RAY DIFFRACTION5CHAIN A AND (RESID 294:323)
6X-RAY DIFFRACTION6CHAIN A AND (RESID 324:344)
7X-RAY DIFFRACTION7CHAIN A AND (RESID 345:380)
8X-RAY DIFFRACTION8CHAIN A AND (RESID 381:386)
9X-RAY DIFFRACTION9CHAIN A AND (RESID 387:429)
10X-RAY DIFFRACTION10CHAIN A AND (RESID 430:444)
11X-RAY DIFFRACTION11CHAIN B AND (RESID 230:241)
12X-RAY DIFFRACTION12CHAIN B AND (RESID 242:269)
13X-RAY DIFFRACTION13CHAIN B AND (RESID 270:284)
14X-RAY DIFFRACTION14CHAIN B AND (RESID 285:300)
15X-RAY DIFFRACTION15CHAIN B AND (RESID 301:323)
16X-RAY DIFFRACTION16CHAIN B AND (RESID 324:344)
17X-RAY DIFFRACTION17CHAIN B AND (RESID 345:365)
18X-RAY DIFFRACTION18CHAIN B AND (RESID 366:407)
19X-RAY DIFFRACTION19CHAIN B AND (RESID 408:422)
20X-RAY DIFFRACTION20CHAIN B AND (RESID 423:444)

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