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- PDB-6s3d: Structure of D25 Fab in complex with scaffold S0_2.126 -

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Basic information

Entry
Database: PDB / ID: 6s3d
TitleStructure of D25 Fab in complex with scaffold S0_2.126
Components
  • Heavy Chain
  • Light Chain
  • S0_2.126
KeywordsANTIVIRAL PROTEIN / hRSV / D25 / Fab fragment
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsCramer, J.T. / Krey, T.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and ResearchGerman Center of Infection Research, Hannover-Braunschweig site Germany
CitationJournal: Science / Year: 2020
Title: De novo protein design enables the precise induction of RSV-neutralizing antibodies.
Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. ...Authors: Sesterhenn, F. / Yang, C. / Bonet, J. / Cramer, J.T. / Wen, X. / Wang, Y. / Chiang, C.I. / Abriata, L.A. / Kucharska, I. / Castoro, G. / Vollers, S.S. / Galloux, M. / Dheilly, E. / Rosset, S. / Corthesy, P. / Georgeon, S. / Villard, M. / Richard, C.A. / Descamps, D. / Delgado, T. / Oricchio, E. / Rameix-Welti, M.A. / Mas, V. / Ervin, S. / Eleouet, J.F. / Riffault, S. / Bates, J.T. / Julien, J.P. / Li, Y. / Jardetzky, T. / Krey, T. / Correia, B.E.
History
DepositionJun 25, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 22, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 27, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.3Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heavy Chain
B: Light Chain
C: Heavy Chain
D: Light Chain
E: Heavy Chain
F: Light Chain
H: Heavy Chain
L: Light Chain
M: S0_2.126
N: S0_2.126
O: S0_2.126
P: S0_2.126


Theoretical massNumber of molelcules
Total (without water)234,63912
Polymers234,63912
Non-polymers00
Water00
1
A: Heavy Chain
B: Light Chain
N: S0_2.126


Theoretical massNumber of molelcules
Total (without water)58,6603
Polymers58,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-34 kcal/mol
Surface area21340 Å2
MethodPISA
2
C: Heavy Chain
D: Light Chain
M: S0_2.126


Theoretical massNumber of molelcules
Total (without water)58,6603
Polymers58,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-36 kcal/mol
Surface area21890 Å2
MethodPISA
3
E: Heavy Chain
F: Light Chain
O: S0_2.126


Theoretical massNumber of molelcules
Total (without water)58,6603
Polymers58,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-31 kcal/mol
Surface area21680 Å2
MethodPISA
4
H: Heavy Chain
L: Light Chain
P: S0_2.126


Theoretical massNumber of molelcules
Total (without water)58,6603
Polymers58,6603
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5140 Å2
ΔGint-34 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.272, 126.977, 156.091
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
Heavy Chain


Mass: 25749.963 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Light Chain


Mass: 24700.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein
S0_2.126


Mass: 8209.471 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli BL21(DE3) (bacteria)
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: 2.74 Å3/Da / Density % sol: 55.05 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% (w/v) PEG 8000, 100 mM HEPES pH 7.5, 200 mM Calcium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS EIGER X 4M / Detector: PIXEL / Date: Aug 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 3→49.086 Å / Num. obs: 96992 / % possible obs: 99.7 % / Redundancy: 7.238 % / Biso Wilson estimate: 65.981 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.156 / Rrim(I) all: 0.168 / Χ2: 1.09 / Net I/σ(I): 8.69
Reflection shell
Resolution (Å)Mean I/σ(I) obsNum. unique obsCC1/2Diffraction-ID% possible all
3-3.081.3871830.81199.3
3.08-3.1669711
3.16-3.2568721
3.25-3.3564181
3.35-3.4664181
3.46-3.5862021
3.58-3.7260331
3.72-3.8757331
3.87-4.0455101
4.04-4.2452491
4.24-4.4749001
4.47-4.7447601
4.74-5.0744881
5.07-5.4741391
5.47-5.9938311
5.99-6.730311
6.7-7.7430311
7.74-9.4825991
9.48-13.4119821
13.41-49.08628.981048196.7

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSBUILT=20190315data reduction
XSCALEBUILT=20190315data scaling
PHASER2.8.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jha

4jha


Resolution: 3→49.086 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 43.01
RfactorNum. reflection% reflection
Rfree0.2917 2515 5 %
Rwork0.269 --
obs0.2702 50267 98.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3→49.086 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14439 0 0 0 14439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00414762
X-RAY DIFFRACTIONf_angle_d0.79320129
X-RAY DIFFRACTIONf_dihedral_angle_d4.0428837
X-RAY DIFFRACTIONf_chiral_restr0.052338
X-RAY DIFFRACTIONf_plane_restr0.0062575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.05770.44481380.39632611X-RAY DIFFRACTION99
3.0577-3.12010.37211380.36312617X-RAY DIFFRACTION99
3.1201-3.1880.37671390.34022649X-RAY DIFFRACTION99
3.188-3.26210.39961380.33232639X-RAY DIFFRACTION100
3.2621-3.34370.3391400.32062638X-RAY DIFFRACTION99
3.3437-3.43410.36771380.31732646X-RAY DIFFRACTION100
3.4341-3.53510.36191400.29732646X-RAY DIFFRACTION100
3.5351-3.64910.35821400.27852663X-RAY DIFFRACTION100
3.6491-3.77950.28761390.27412627X-RAY DIFFRACTION99
3.7795-3.93080.34241400.27842667X-RAY DIFFRACTION100
3.9308-4.10960.31461400.272682X-RAY DIFFRACTION100
4.1096-4.32620.24611380.24682598X-RAY DIFFRACTION97
4.3262-4.5970.2611380.222632X-RAY DIFFRACTION98
4.597-4.95160.19331410.21592688X-RAY DIFFRACTION100
4.9516-5.44940.25431420.24212706X-RAY DIFFRACTION100
5.4494-6.23650.33331430.25342713X-RAY DIFFRACTION100
6.2365-7.85220.2871460.28152754X-RAY DIFFRACTION100
7.8522-49.09210.23251370.25122576X-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)
13.5245-1.9878-1.79964.24371.65832.3918-0.7074-0.7553-0.84371.47890.38150.85271.1291-0.06070.32190.81670.03550.44470.64410.28860.8851-25.4056-14.93635.0415
23.3416-1.7972-1.84364.60842.54113.1814-0.2706-0.3823-0.12890.12880.01680.9750.1889-0.07320.23730.64730.0873-0.0830.39120.10561.1259-32.40792.5789-0.0149
34.30072.5478-0.42833.9375-2.39282.28250.153-1.6888-1.32960.443-0.3948-1.19570.45920.33130.2621.10030.0218-0.09890.95890.72070.955314.9858-26.30564.9966
44.13371.8623-0.03562.4427-0.77612.4368-0.123-0.6659-1.61260.0797-0.38820.05240.3568-0.11490.36350.6579-0.02050.17590.48580.39050.8568-2.3695-32.8363-0.7973
55.89693.63532.6337.18752.88223.81290.5138-1.46311.26811.3672-1.0051.09750.3304-0.58210.51880.7414-0.16660.24980.7744-0.11920.937-14.845526.20494.9147
66.45690.89652.54114.94190.41212.0172-0.0902-0.50511.38840.6893-0.17370.50060.08140.13870.29480.84840.00550.04440.4260.10.8952.558332.846-0.9786
73.9791-3.00832.47546.2371-2.31922.3101-0.965-1.51451.28671.46290.9724-2.43580.2478-0.25350.0661.6610.3702-0.16720.8090.13610.729125.531414.97915.0854
81.934-1.3143-0.20793.7628-0.13341.5026-0.0944-0.2369-0.69720.84830.2234-1.66780.53080.004-0.03121.0269-0.0647-0.64090.54910.51960.954832.5402-2.53150.1329
97.7408-1.01240.58493.69081.38839.3524-0.27742.5091-0.4204-1.3427-0.1197-2.1521-0.31041.04960.18961.0853-0.18910.72521.2133-0.05331.498926.523-20.7525-30.1709
106.83720.8788-0.17938.78130.35046.42980.24661.3864-1.3101-2.43770.24090.55780.5913-0.2052-0.33351.60160.0435-0.27760.8712-0.35250.9887-21.2786-26.393-29.8252
116.1394-1.76932.67817.21460.0318.1998-0.33591.46850.8217-1.6739-0.16520.4076-0.9884-0.4760.35451.0934-0.13-0.29541.20060.35051.0974-26.778220.9471-30.003
123.13240.31070.65766.5908-2.24797.5076-0.32051.03060.5993-2.55940.3821-0.4114-1.39770.1107-0.22821.66180.23760.31480.86640.43411.148521.585126.3953-29.9269
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain 'A' and resid 4 through 224)
2X-RAY DIFFRACTION2(chain 'B' and resid 3 through 213)
3X-RAY DIFFRACTION3(chain 'C' and resid 4 through 228)
4X-RAY DIFFRACTION4(chain 'D' and resid 2 through 213)
5X-RAY DIFFRACTION5(chain 'E' and resid 4 through 228)
6X-RAY DIFFRACTION6(chain 'F' and resid 3 through 213)
7X-RAY DIFFRACTION7(chain 'H' and resid 4 through 222)
8X-RAY DIFFRACTION8(chain 'L' and resid 3 through 213)
9X-RAY DIFFRACTION9(chain 'M' and resid 2 through 60)
10X-RAY DIFFRACTION10(chain 'N' and resid 2 through 59)
11X-RAY DIFFRACTION11(chain 'O' and resid 2 through 60)
12X-RAY DIFFRACTION12(chain 'P' and resid 2 through 59)

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