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- PDB-7wvi: Crystal structure of SIA28 -

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Basic information

Entry
Database: PDB / ID: 7wvi
TitleCrystal structure of SIA28
Components
  • Heavy chain of SIA28
  • Light chain of SIA28
KeywordsVIRUS with monoclonal antibody / Influenza Virus / Hemagglutinin / Monoclonal antibody / VIRUS
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.48 Å
AuthorsChen, Y. / Qi, J. / Gao, G.F.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nat Commun / Year: 2022
Title: Structural basis for a human broadly neutralizing influenza A hemagglutinin stem-specific antibody including H17/18 subtypes.
Authors: Chen, Y. / Wang, F. / Yin, L. / Jiang, H. / Lu, X. / Bi, Y. / Zhang, W. / Shi, Y. / Burioni, R. / Tong, Z. / Song, H. / Qi, J. / Gao, G.F.
History
DepositionFeb 10, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 18, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heavy chain of SIA28
B: Light chain of SIA28
C: Heavy chain of SIA28
D: Light chain of SIA28


Theoretical massNumber of molelcules
Total (without water)94,1934
Polymers94,1934
Non-polymers00
Water4,846269
1
A: Heavy chain of SIA28
B: Light chain of SIA28


Theoretical massNumber of molelcules
Total (without water)47,0972
Polymers47,0972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-28 kcal/mol
Surface area20130 Å2
MethodPISA
2
C: Heavy chain of SIA28
D: Light chain of SIA28


Theoretical massNumber of molelcules
Total (without water)47,0972
Polymers47,0972
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-27 kcal/mol
Surface area20200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.560, 86.361, 82.895
Angle α, β, γ (deg.)90.000, 105.290, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody Heavy chain of SIA28


Mass: 23965.982 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
#2: Antibody Light chain of SIA28


Mass: 23130.760 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Mammalian expression vector EGFP-MCS-pcDNA3.1 (others)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O

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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: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES 12% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 36196 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.05 Å2 / CC1/2: 0.986 / Net I/σ(I): 15.3
Reflection shellResolution: 2.5→2.59 Å / Num. unique obs: 3596 / CC1/2: 0.658

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4X0K

4x0k


Resolution: 2.48→42.14 Å / SU ML: 0.2392 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.7678
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2298 1810 5 %
Rwork0.1949 34357 -
obs0.1967 36167 97.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 35.53 Å2
Refinement stepCycle: LAST / Resolution: 2.48→42.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6628 0 0 269 6897
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00326788
X-RAY DIFFRACTIONf_angle_d0.65559234
X-RAY DIFFRACTIONf_chiral_restr0.0471044
X-RAY DIFFRACTIONf_plane_restr0.00441178
X-RAY DIFFRACTIONf_dihedral_angle_d14.84342418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.550.29051000.26131993X-RAY DIFFRACTION73.59
2.55-2.620.27861520.24852647X-RAY DIFFRACTION99.93
2.62-2.710.27421560.2462669X-RAY DIFFRACTION99.96
2.71-2.810.30311530.24432652X-RAY DIFFRACTION99.89
2.81-2.920.29031460.25012677X-RAY DIFFRACTION100
2.92-3.050.27721370.22312702X-RAY DIFFRACTION100
3.05-3.210.28721210.21632741X-RAY DIFFRACTION100
3.21-3.410.22011270.20432704X-RAY DIFFRACTION99.96
3.41-3.680.23611240.18942688X-RAY DIFFRACTION100
3.68-4.050.24041470.1792720X-RAY DIFFRACTION99.97
4.05-4.630.17881480.14932716X-RAY DIFFRACTION99.86
4.63-5.830.16941590.15632685X-RAY DIFFRACTION99.75
5.83-42.140.19071400.17672763X-RAY DIFFRACTION99.38
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)
10.620869354441-0.2007240651050.5100958825470.4347968262180.4863397111833.016210505780.00936595231805-0.0649116699072-0.05046932698850.0250471693101-0.05937891137950.06102135186710.0583081454962-0.3029429142470.03884068661470.143937368243-0.01851737776520.02588251125110.267528275408-0.01988931194080.22631215031911.4560835524-11.384772823322.7124387164
21.233925281780.05715355076950.7634005124890.4497774948210.2810915827912.01776940587-0.04219170622180.04584446803520.0608738601005-0.0554127392756-0.03673536859220.0184244166859-0.178085606678-0.05793010968380.07953970881910.1697395491180.01263278497810.02091054960490.1682152257580.01075591101560.2336723257326.4885003693-1.6299467106522.8185088026
30.815455419851-0.2554479142960.5049717519360.596437092414-0.1668678966572.87761484780.03792924711830.14559805231-0.0164109223961-0.0605871582257-0.0177147777992-0.04677299040860.05351865175350.0788072871021-0.02092568981560.1413307752980.01167056918510.01259057581910.14937242067-0.01099817211990.22045022865660.2206499182-18.113767963134.3349845439
41.035095143540.08926416255560.8165274931960.4009576924970.1223156008651.66072834627-0.02039338025770.08736743011870.000665238650502-0.03138493426130.01540900120730.0467533880444-0.02970743994140.00949316814629-0.00647180921930.1544919146550.01670129936350.02542894883690.151949034043-0.001063572557070.2034131959149.1625683844-4.4213815287631.0509201945
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain AAA1 - 2261 - 226
22chain BBB1 - 2141 - 214
33chain CCC1 - 2261 - 226
44chain DDD1 - 2141 - 214

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