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- PDB-5wca: Crystal structure of the broadly neutralizing Influenza A antibod... -

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Basic information

Entry
Database: PDB / ID: 5wca
TitleCrystal structure of the broadly neutralizing Influenza A antibody VRC 315 27-1C08 Fab.
Components
  • VRC315 27-1C08 Fab Heavy chain
  • VRC315 27-1C08 Fab Light chain
KeywordsIMMUNE SYSTEM / antibody / influenza / human vaccine trial
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.369 Å
AuthorsJoyce, M.G. / Andrews, S.F. / Mascola, J.R. / McDermott, A.B. / Kwong, P.D.
CitationJournal: Sci Immunol / Year: 2017
Title: Preferential induction of cross-group influenza A hemagglutinin stem-specific memory B cells after H7N9 immunization in humans.
Authors: Andrews, S.F. / Joyce, M.G. / Chambers, M.J. / Gillespie, R.A. / Kanekiyo, M. / Leung, K. / Yang, E.S. / Tsybovsky, Y. / Wheatley, A.K. / Crank, M.C. / Boyington, J.C. / Prabhakaran, M.S. / ...Authors: Andrews, S.F. / Joyce, M.G. / Chambers, M.J. / Gillespie, R.A. / Kanekiyo, M. / Leung, K. / Yang, E.S. / Tsybovsky, Y. / Wheatley, A.K. / Crank, M.C. / Boyington, J.C. / Prabhakaran, M.S. / Narpala, S.R. / Chen, X. / Bailer, R.T. / Chen, G. / Coates, E. / Kwong, P.D. / Koup, R.A. / Mascola, J.R. / Graham, B.S. / Ledgerwood, J.E. / McDermott, A.B.
History
DepositionJun 29, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 28, 2018Group: Data collection / Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.3Oct 4, 2023Group: 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 23, 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
H: VRC315 27-1C08 Fab Heavy chain
L: VRC315 27-1C08 Fab Light chain


Theoretical massNumber of molelcules
Total (without water)46,7502
Polymers46,7502
Non-polymers00
Water13,727762
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-22 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.647, 73.780, 70.877
Angle α, β, γ (deg.)90.00, 93.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody VRC315 27-1C08 Fab Heavy chain


Mass: 24283.303 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody VRC315 27-1C08 Fab Light chain


Mass: 22466.805 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 762 / Source method: isolated from a natural source / Formula: H2O
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: 2.38 Å3/Da / Density % sol: 48.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 22% PEG-8000, 25% isopropanol, 0.1 M imidazole, pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 13, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.369→35.389 Å / Num. obs: 90935 / % possible obs: 98.3 % / Redundancy: 3.6 % / Net I/σ(I): 17.35

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5TY6

5ty6


Resolution: 1.369→35.389 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.62
RfactorNum. reflection% reflection
Rfree0.1816 4553 5.01 %
Rwork0.1653 --
obs0.1661 90919 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.369→35.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 0 762 4025
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053370
X-RAY DIFFRACTIONf_angle_d0.8554608
X-RAY DIFFRACTIONf_dihedral_angle_d15.9081212
X-RAY DIFFRACTIONf_chiral_restr0.074528
X-RAY DIFFRACTIONf_plane_restr0.005584
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3691-1.38470.30671130.29172419X-RAY DIFFRACTION83
1.3847-1.40090.27491510.2842821X-RAY DIFFRACTION97
1.4009-1.4180.29361370.25182899X-RAY DIFFRACTION98
1.418-1.4360.25751520.24312804X-RAY DIFFRACTION98
1.436-1.45490.21161500.22872837X-RAY DIFFRACTION98
1.4549-1.47480.2921540.21972918X-RAY DIFFRACTION98
1.4748-1.49590.24931590.22182804X-RAY DIFFRACTION99
1.4959-1.51820.22171690.20562889X-RAY DIFFRACTION99
1.5182-1.54190.23731230.19752885X-RAY DIFFRACTION98
1.5419-1.56720.20851560.19092849X-RAY DIFFRACTION99
1.5672-1.59420.21191520.1862884X-RAY DIFFRACTION99
1.5942-1.62320.19781700.18342863X-RAY DIFFRACTION99
1.6232-1.65440.20811720.17732887X-RAY DIFFRACTION99
1.6544-1.68820.20281440.18042885X-RAY DIFFRACTION99
1.6882-1.72490.24221540.17872897X-RAY DIFFRACTION99
1.7249-1.7650.2151380.17162917X-RAY DIFFRACTION99
1.765-1.80920.19531790.16642865X-RAY DIFFRACTION100
1.8092-1.85810.16481460.16392914X-RAY DIFFRACTION100
1.8581-1.91280.16141340.15942897X-RAY DIFFRACTION100
1.9128-1.97450.20071560.15772924X-RAY DIFFRACTION100
1.9745-2.04510.1691530.16252927X-RAY DIFFRACTION100
2.0451-2.12690.17261480.16082913X-RAY DIFFRACTION100
2.1269-2.22370.18121790.1592880X-RAY DIFFRACTION100
2.2237-2.34090.16441640.16122888X-RAY DIFFRACTION100
2.3409-2.48760.17581380.16432949X-RAY DIFFRACTION100
2.4876-2.67960.19731420.16892947X-RAY DIFFRACTION100
2.6796-2.94910.18031640.16642925X-RAY DIFFRACTION100
2.9491-3.37560.16441450.15492937X-RAY DIFFRACTION100
3.3756-4.25170.15561580.14392955X-RAY DIFFRACTION100
4.2517-35.40060.1561530.14492987X-RAY DIFFRACTION100
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)
10.35160.03140.10880.53230.16520.1074-0.10660.001-0.32070.1120.1394-0.17290.01520.08610.03860.12740.0258-0.00650.1616-0.06170.21377.8325-8.979317.5633
20.7308-0.2422-0.1041.48340.29630.8625-0.07630.2146-0.1233-0.04820.1485-0.05270.03830.02450.09850.1004-0.01970.00660.1629-0.0530.130.6854-7.45068.8253
31.51460.1873-0.66552.54890.68322.02670.1036-0.12610.15430.335-0.01510.0598-0.0309-0.002-0.04160.15970.00440.02120.0693-0.01190.150915.64554.765434.9414
40.2973-0.10310.07910.9802-0.05590.1505-0.10220.3475-0.0077-0.43750.1963-0.3477-0.1213-0.0728-0.00190.2704-0.05380.03550.2954-0.00450.1576-0.473814.1052-0.2316
50.5063-0.05720.35971.5556-0.08260.3088-0.11340.05160.0278-0.03990.17120.0714-0.0941-0.1520.01610.1406-0.0128-0.00310.20170.03520.1169-5.658412.58429.0794
60.95520.43240.12820.7692-0.13660.7023-0.1005-0.01060.03880.05040.0101-0.1212-0.1207-0.0591-0.40720.09560.02030.0210.0341-0.02240.042113.544212.305522.5333
72.1266-0.44210.48172.5918-0.01031.9682-0.0333-0.06820.0465-0.0172-0.005-0.2472-0.2610.10230.01940.1483-0.0148-0.00170.0673-0.00750.08925.314818.733130.5318
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 17 )
2X-RAY DIFFRACTION2chain 'H' and (resid 18 through 111 )
3X-RAY DIFFRACTION3chain 'H' and (resid 112 through 214 )
4X-RAY DIFFRACTION4chain 'L' and (resid 3 through 32 )
5X-RAY DIFFRACTION5chain 'L' and (resid 33 through 91 )
6X-RAY DIFFRACTION6chain 'L' and (resid 92 through 129 )
7X-RAY DIFFRACTION7chain 'L' and (resid 130 through 209 )

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