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- PDB-8zcm: Cryogenic Temperature Crystal Structure of Fc Fragment of Human I... -

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Basic information

Entry
Database: PDB / ID: 8zcm
TitleCryogenic Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap
ComponentsImmunoglobulin gamma-1 heavy chain
KeywordsIMMUNE SYSTEM / fusion protein / immunoglobin / N-glycans
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/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain ...Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulin subtype / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsDestan, E. / DeMirci, H.
Funding support Turkey, 1items
OrganizationGrant numberCountry
Other government119C132 Turkey
CitationJournal: To Be Published
Title: Cryogenic Temperature Crystal Structure of Fc Fragment of Human IgG1 from Biosimilar VEGF-Trap
Authors: Destan, E. / DeMirci, H.
History
DepositionApr 30, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

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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)50,2475
Polymers47,2692
Non-polymers2,9783
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7460 Å2
ΔGint43 kcal/mol
Surface area21890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.450, 79.620, 125.540
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-(1-3)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-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)-[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
DGalpb1-4DGlcpNAcb1-3DManpa1-6[DGlcpNAcb1-2DManpa1-3]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_d2-e1_f3-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]{[(2+1)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(3+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: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 298 K / Method: batch mode
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: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Nov 16, 2023
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.64→46.01 Å / Num. obs: 14547 / % possible obs: 95.5 % / Redundancy: 2.85 % / CC1/2: 0.993 / Rmerge(I) obs: 0.106 / Rrim(I) all: 0.128 / Net I/σ(I): 7.55
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rrim(I) allDiffraction-ID
2.64-2.80.87623410.4411.0711
2.8-2.990.57821310.5740.721
2.99-3.230.3220620.850.3921
3.23-3.540.18518670.9380.2251
3.54-3.960.13117330.9670.1571
3.96-4.570.07615250.9890.0911
4.57-5.60.06413100.990.0771
5.6-7.920.0610090.9930.0731

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XSCALEdata scaling
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.64→46.01 Å / SU ML: 0.73 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 49.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.4093 1454 10.01 %
Rwork0.354 --
obs0.3597 14531 95.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.64→46.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3312 0 201 29 3542
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033624
X-RAY DIFFRACTIONf_angle_d0.5474940
X-RAY DIFFRACTIONf_dihedral_angle_d12.5431409
X-RAY DIFFRACTIONf_chiral_restr0.046595
X-RAY DIFFRACTIONf_plane_restr0.004608
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.730.39781450.36551303X-RAY DIFFRACTION98
2.73-2.840.43491440.37361300X-RAY DIFFRACTION97
2.84-2.970.41361420.39781270X-RAY DIFFRACTION96
2.97-3.130.42281460.42081315X-RAY DIFFRACTION96
3.13-3.330.5031390.43421264X-RAY DIFFRACTION94
3.33-3.580.51291440.40141295X-RAY DIFFRACTION96
3.58-3.940.49181480.37141322X-RAY DIFFRACTION97
3.94-4.510.37621470.35511330X-RAY DIFFRACTION96
4.51-5.680.36161470.31791320X-RAY DIFFRACTION96
5.69-46.010.34191520.29421358X-RAY DIFFRACTION92
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)
11.2689-0.14770.79640.3816-0.37811.3715-0.14171.66560.271-0.84470.4136-0.4932-0.03660.30290.57712.1495-0.49711.13221.90840.51621.4885-6.898412.37342.5276
21.6417-0.21410.32172.58610.04062.125-0.6168-0.3702-0.15651.01310.20280.25420.2641-0.08220.13720.6260.15660.25340.5847-0.07640.3006-6.056310.448334.2809
31.7895-0.1872-0.78452.50160.90012.75060.0721-0.2728-0.0986-0.011-0.34440.2392-0.2868-0.0117-0.31730.41970.1950.33570.43390.19720.679116.1184-12.681419.0485
41.15210.24970.0390.449-0.23320.382-0.40830.4576-0.28-0.24910.1797-0.0930.25090.040.11940.4363-0.08510.18551.45230.60360.593619.3516-15.47551.4477
53.94781.88962.70776.41391.69874.5417-0.29890.4130.8204-0.4103-0.59581.260.22390.03730.74671.07760.2689-0.19160.6186-0.05510.751916.4061-18.73646.5639
60.82970.11580.36091.3464-0.24860.8224-0.41810.33890.5638-0.7645-0.13950.0309-0.06910.48910.10280.351-0.3773-0.04620.28860.29080.293723.0001-10.012512.3924
70.85990.22361.16012.3837-0.09261.6313-0.06380.21630.53080.0554-0.62630.0690.2714-0.35360.29291.27610.24750.05070.5853-0.11490.55853.68491.107938.2395
81.06440.12970.57941.80560.46821.3502-0.0836-0.1128-0.16980.4491-0.17410.14340.081-0.2672-0.01530.71070.193-0.04510.5012-0.15980.26892.5556-4.525136.0459
91.2959-2.10.40455.1212-2.12332.5262-0.1786-0.4461-0.15091.12191.01320.574-0.5945-0.2780.20870.95020.41920.01310.8805-0.22380.43822.3947-9.363444.3015
100.14640.3525-0.55590.8614-1.1622.3727-0.1108-1.0153-0.5733-0.15620.21520.1470.2330.10930.06531.3850.1486-0.32860.80140.27610.440613.0111-6.202141.8354
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 223 through 321 )
2X-RAY DIFFRACTION2chain 'A' and (resid 322 through 428 )
3X-RAY DIFFRACTION3chain 'B' and (resid 222 through 249 )
4X-RAY DIFFRACTION4chain 'B' and (resid 250 through 264 )
5X-RAY DIFFRACTION5chain 'B' and (resid 265 through 286 )
6X-RAY DIFFRACTION6chain 'B' and (resid 287 through 321 )
7X-RAY DIFFRACTION7chain 'B' and (resid 322 through 357 )
8X-RAY DIFFRACTION8chain 'B' and (resid 358 through 403 )
9X-RAY DIFFRACTION9chain 'B' and (resid 404 through 413 )
10X-RAY DIFFRACTION10chain 'B' and (resid 414 through 428 )

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