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Basic information

Entry
Database: PDB / ID: 9iie
TitleCryogenic Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / N-glycans / immunoglobulin
Function / homology
Function and homology information


immunoglobulin complex / adaptive immune response / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set ...: / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / 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
Similarity search - Domain/homology
Immunoglobulin gamma-1 heavy chain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.14 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government Turkey
CitationJournal: Small Struct / Year: 2025
Title: Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap
Authors: Destan, E. / Turkut, E. / Aldeniz, A. / Kang, J. / Tosha, T. / Yabashi, M. / Yilmaz, B. / Timucin, C. / Matsuura, H. / Kawano, Y. / Cinkaya, I. / Demirci, H.
History
DepositionJun 20, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2May 21, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Immunoglobulin gamma-1 heavy chain
B: Immunoglobulin gamma-1 heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1554
Polymers47,2692
Non-polymers2,8862
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7490 Å2
ΔGint54 kcal/mol
Surface area21820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.920, 80.480, 137.070
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: Antibody Immunoglobulin gamma-1 heavy chain / Immunoglobulin gamma-1 heavy chain NIE


Mass: 23634.676 Da / Num. of mol.: 2 / Fragment: Fc Fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P0DOX5
#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-(1-3)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1625.490 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-6[DGlcpNAcb1-3DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1b_1-5]/1-1-2-3-1-3-1-4-5/a4-b1_a6-i1_b4-c1_c3-d1_c6-f1_d3-e1_f2-g1_g4-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(3+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose- ...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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1260.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam 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][a1221m-1a_1-5]/1-1-2-3-3-1-4/a4-b1_a6-g1_b4-c1_c3-d1_c6-e1_e2-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-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]{}}}}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.93 Å3/Da / Density % sol: 58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 0.1M Bis-Tris pH 6.5, 25% w/v Polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU PhotonJet-R / Wavelength: 1 Å
DetectorType: RIGAKU HyPix-Arc 150 / Detector: PIXEL / Date: Jun 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.14→137.08 Å / Num. obs: 9844 / % possible obs: 96.5 % / Redundancy: 3.6 % / CC1/2: 0.748 / CC star: 0.925 / Net I/σ(I): 2.26
Reflection shellResolution: 3.14→3.22 Å / Redundancy: 3.9 % / Num. unique obs: 683 / CC1/2: 0.155 / CC star: 0.518 / % possible all: 98.6

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.14→23.84 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 0.02 / Phase error: 29.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3086 805 10 %
Rwork0.2567 --
obs0.2621 8053 79.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.14→23.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 195 30 3543
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033605
X-RAY DIFFRACTIONf_angle_d0.5034912
X-RAY DIFFRACTIONf_dihedral_angle_d14.4071396
X-RAY DIFFRACTIONf_chiral_restr0.043593
X-RAY DIFFRACTIONf_plane_restr0.004604
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.14-3.340.41331180.34951063X-RAY DIFFRACTION72
3.34-3.590.37321210.29551096X-RAY DIFFRACTION74
3.59-3.950.30981270.2611139X-RAY DIFFRACTION76
3.95-4.520.29921310.23411176X-RAY DIFFRACTION77
4.52-5.680.25291450.21991316X-RAY DIFFRACTION86
5.68-23.840.26721630.23181458X-RAY DIFFRACTION90
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)
10.4366-0.2767-0.01731.7609-1.30991.335-0.26530.18170.2157-0.63430.1111-0.37770.24250.1562-0.02970.3129-0.2653-0.00570.2930.00120.2999-9.218212.923715.7762
25.4173-2.5911-1.30611.86162.17645.5144-0.00481.43050.0176-0.8907-0.3941-0.6647-1.04660.5640.22831.25550.06570.47751.19010.07910.6962-5.630112.9641-2.177
30.5774-1.21790.07923.3215-0.83860.61010.40880.5737-0.2934-0.8512-0.25910.5090.51430.084-0.19041.41420.4243-0.40580.88890.25781.2281-16.452316.3024.8118
43.85662.3937-1.01197.1037-3.72935.2490.0223-0.2208-0.1850.3438-0.2062-0.25680.05580.13210.17541.5242-0.35410.47281.21040.54821.33126.640516.54493.1534
52.11520.0361-0.54461.48410.18821.1974-0.0248-0.00010.3572-0.1196-0.0140.1054-0.19670.1380.01480.28660.07840.01550.19530.03110.1167-7.40698.468431.2116
61.4892-0.2169-1.37491.21440.54797.8547-0.11390.2221-0.3807-0.1249-0.08150.10230.0889-0.8636-0.01930.12650.01540.15770.19-0.04320.205613.0002-11.421718.3934
71.36510.5635-0.15611.85070.48160.1985-0.18490.2119-0.1665-0.4788-0.08490.0371-0.25020.03760.1930.3544-0.08960.17610.0876-0.12310.358416.1254-16.15689.4336
81.43820.79150.13920.87260.55060.5235-0.0584-0.11140.13730.20290.2237-0.3358-0.04280.0676-0.01010.25490.17730.08080.14610.01050.314425.3924-17.276911.7663
90.60961.1272-0.24672.6426-1.55442.25280.4712-0.2005-0.1212-0.32270.22930.6070.9618-0.7616-0.57950.3235-0.1243-0.07060.30090.00470.28644.7021-20.84992.2603
100.53090.31020.41931.8380.9181.3031-0.1986-0.19260.0787-0.2713-0.09710.17310.08750.1105-0.0968-0.01990.1010.12810.21090.0640.178820.4832-8.399516.2492
115.56610.6910.05180.561-1.10663.3420.0495-0.2280.17290.2623-0.0324-0.1414-0.2763-0.093-0.07040.18140.06640.19520.4683-0.07350.6138-4.9916-1.612247.5712
122.3324-0.46851.38372.9002-0.20763.063-0.3007-0.68220.0173-0.10350.2025-0.15470.3555-0.27010.06520.20790.00820.07210.22520.06230.29213.6122-8.641438.8277
134.14460.7883-0.19882.41661.03271.9514-0.0933-0.65340.09140.54670.00140.26480.0707-0.17490.10140.31120.19190.02550.1815-0.04930.12620.6823-2.780239.1929
145.2325-2.1703-2.67791.45112.43894.5733-0.5275-0.8039-0.73630.68620.5436-0.13160.98380.2187-0.06120.52530.1024-0.17710.27490.14250.62349.2908-9.921944.8588
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 249 )
2X-RAY DIFFRACTION2chain 'A' and (resid 250 through 264 )
3X-RAY DIFFRACTION3chain 'A' and (resid 265 through 275 )
4X-RAY DIFFRACTION4chain 'A' and (resid 276 through 286 )
5X-RAY DIFFRACTION5chain 'A' and (resid 287 through 429 )
6X-RAY DIFFRACTION6chain 'B' and (resid 222 through 236 )
7X-RAY DIFFRACTION7chain 'B' and (resid 237 through 264 )
8X-RAY DIFFRACTION8chain 'B' and (resid 265 through 275 )
9X-RAY DIFFRACTION9chain 'B' and (resid 276 through 286 )
10X-RAY DIFFRACTION10chain 'B' and (resid 287 through 331 )
11X-RAY DIFFRACTION11chain 'B' and (resid 332 through 346 )
12X-RAY DIFFRACTION12chain 'B' and (resid 347 through 378 )
13X-RAY DIFFRACTION13chain 'B' and (resid 379 through 403 )
14X-RAY DIFFRACTION14chain 'B' and (resid 404 through 428 )

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