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- PDB-6hkg: Structure of FISW84 Fab Fragment -

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Basic information

Entry
Database: PDB / ID: 6hkg
TitleStructure of FISW84 Fab Fragment
Components
  • (FISW84 Fab Fragment Heavy ...) x 2
  • (FISW84 Fab Fragment Light ...) x 2
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 Å
AuthorsBenton, D.J. / Rosenthal, P.B.
Funding support United Kingdom, 7items
OrganizationGrant numberCountry
Cancer Research UKFC001078 United Kingdom
Cancer Research UKFC001143 United Kingdom
Medical Research Council (United Kingdom)FC001078 United Kingdom
Medical Research Council (United Kingdom)FC001143 United Kingdom
Wellcome TrustFC001078 United Kingdom
Wellcome TrustFC001143 United Kingdom
European Research Council629829 United Kingdom
CitationJournal: Proc Natl Acad Sci U S A / Year: 2018
Title: Influenza hemagglutinin membrane anchor.
Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / ...Authors: Donald J Benton / Andrea Nans / Lesley J Calder / Jack Turner / Ursula Neu / Yi Pu Lin / Esther Ketelaars / Nicole L Kallewaard / Davide Corti / Antonio Lanzavecchia / Steven J Gamblin / Peter B Rosenthal / John J Skehel /
Abstract: Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the ...Viruses with membranes fuse them with cellular membranes, to transfer their genomes into cells at the beginning of infection. For Influenza virus, the membrane glycoprotein involved in fusion is the hemagglutinin (HA), the 3D structure of which is known from X-ray crystallographic studies. The soluble ectodomain fragments used in these studies lacked the "membrane anchor" portion of the molecule. Since this region has a role in membrane fusion, we have determined its structure by analyzing the intact, full-length molecule in a detergent micelle, using cryo-EM. We have also compared the structures of full-length HA-detergent micelles with full-length HA-Fab complex detergent micelles, to describe an infectivity-neutralizing monoclonal Fab that binds near the ectodomain membrane anchor junction. We determine a high-resolution HA structure which compares favorably in detail with the structure of the ectodomain seen by X-ray crystallography; we detect, clearly, all five carbohydrate side chains of HA; and we find that the ectodomain is joined to the membrane anchor by flexible, eight-residue-long, linkers. The linkers extend into the detergent micelle to join a central triple-helical structure that is a major component of the membrane anchor.
History
DepositionSep 6, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 26, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 10, 2018Group: Data collection / Database references / Structure summary
Category: citation / entity
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.formula_weight
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.formula_weight
Revision 1.3Oct 9, 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: FISW84 Fab Fragment Heavy Chain
B: FISW84 Fab Fragment Light Chain
C: FISW84 Fab Fragment Heavy Chain
D: FISW84 Fab Fragment Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,91710
Polymers84,3404
Non-polymers5766
Water7,332407
1
A: FISW84 Fab Fragment Heavy Chain
B: FISW84 Fab Fragment Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,7176
Polymers46,3332
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-70 kcal/mol
Surface area19470 Å2
MethodPISA
2
C: FISW84 Fab Fragment Heavy Chain
D: FISW84 Fab Fragment Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,2004
Polymers38,0082
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-47 kcal/mol
Surface area16670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.160, 130.160, 167.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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Antibody , 4 types, 4 molecules ABCD

#1: Antibody FISW84 Fab Fragment Heavy Chain


Mass: 23055.055 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)
#2: Antibody FISW84 Fab Fragment Light Chain


Mass: 23277.766 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)
#3: Antibody FISW84 Fab Fragment Heavy Chain


Mass: 20802.520 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)
#4: Antibody FISW84 Fab Fragment Light Chain


Mass: 17205.020 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293 / Production host: Homo sapiens (human)

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Non-polymers , 2 types, 413 molecules

#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.11 Å3/Da / Density % sol: 41.6 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 4.6
Details: 2.04 M ammonium sulfate, 0.1 M sodium acetate pH 4.6 Cryoprotected in 2.1 M ammonium sulfate, 0.1 M sodium acetate pH 4.6 and 25 % (v/v) ethylene glycol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 21, 2014 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.87→29.75 Å / Num. obs: 118143 / % possible obs: 99.6 % / Redundancy: 5.9 % / Biso Wilson estimate: 39.3 Å2 / CC1/2: 0.998 / Rrim(I) all: 0.086 / Net I/σ(I): 11.5
Reflection shellResolution: 1.87→1.92 Å / Redundancy: 5.7 % / Mean I/σ(I) obs: 1 / Num. unique obs: 8595 / CC1/2: 0.288

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2vxs, 2vxv

2vxs

2vxv


Resolution: 1.87→29.749 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.05
RfactorNum. reflection% reflection
Rfree0.1995 5868 4.97 %
Rwork0.1826 --
obs0.1835 118081 99.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.87→29.749 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5854 0 30 407 6291
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076305
X-RAY DIFFRACTIONf_angle_d0.9028636
X-RAY DIFFRACTIONf_dihedral_angle_d10.3153741
X-RAY DIFFRACTIONf_chiral_restr0.061972
X-RAY DIFFRACTIONf_plane_restr0.0051124
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.89120.31131830.32553639X-RAY DIFFRACTION98
1.8912-1.91350.37291910.33793713X-RAY DIFFRACTION100
1.9135-1.93680.34442100.32713651X-RAY DIFFRACTION99
1.9368-1.96130.33841800.29073712X-RAY DIFFRACTION99
1.9613-1.98710.27781950.27533683X-RAY DIFFRACTION100
1.9871-2.01430.28172100.25173690X-RAY DIFFRACTION100
2.0143-2.04310.25661880.2433733X-RAY DIFFRACTION100
2.0431-2.07360.24161900.22833733X-RAY DIFFRACTION100
2.0736-2.1060.29471900.22223703X-RAY DIFFRACTION100
2.106-2.14050.23041890.20963731X-RAY DIFFRACTION100
2.1405-2.17740.22121880.20373702X-RAY DIFFRACTION100
2.1774-2.2170.21641870.19543713X-RAY DIFFRACTION100
2.217-2.25960.20211960.19943730X-RAY DIFFRACTION100
2.2596-2.30570.23551940.18953683X-RAY DIFFRACTION99
2.3057-2.35580.21872000.19093689X-RAY DIFFRACTION99
2.3558-2.41060.21231970.18583732X-RAY DIFFRACTION100
2.4106-2.47080.24041690.18173737X-RAY DIFFRACTION100
2.4708-2.53760.2071880.18673740X-RAY DIFFRACTION100
2.5376-2.61220.2112070.17693740X-RAY DIFFRACTION100
2.6122-2.69650.19462110.17753719X-RAY DIFFRACTION100
2.6965-2.79280.18531900.17463775X-RAY DIFFRACTION100
2.7928-2.90450.21911810.18743740X-RAY DIFFRACTION100
2.9045-3.03660.20922340.18613729X-RAY DIFFRACTION99
3.0366-3.19650.20261850.1763755X-RAY DIFFRACTION99
3.1965-3.39650.18511970.17243763X-RAY DIFFRACTION100
3.3965-3.65840.17762010.15913787X-RAY DIFFRACTION100
3.6584-4.02570.16461770.1583829X-RAY DIFFRACTION100
4.0257-4.60640.15492140.14113795X-RAY DIFFRACTION99
4.6064-5.79650.16532200.1583848X-RAY DIFFRACTION100
5.7965-29.75270.23722060.22094019X-RAY DIFFRACTION99
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)
11.89990.06980.80682.5963-0.39631.62020.03110.09880.051-0.0209-0.0591-0.051-0.0327-0.0129-0.00010.31630.0071-0.05190.36260.03150.34621.0521104.86315.6608
20.02110.02770.01550.0360.00360.02380.0379-0.3741-0.4127-0.0234-0.08850.17230.9531-0.0818-0.00080.5152-0.0407-0.09610.44260.03110.50441.496882.022211.4189
31.7535-0.38620.51512.5599-0.52811.2849-0.1387-0.39340.05580.30050.24830.4172-0.0381-0.4909-0.00720.42930.007-0.00870.59320.02780.5129-0.523688.277233.7257
42.7025-0.031.13342.373-0.85642.0055-0.10960.11310.30560.15270.0154-0.2587-0.23730.2396-00.3596-0.0244-0.08320.35170.03340.459717.6862113.621916.7529
50.0848-0.01250.01090.0432-0.0050.046-0.01430.0930.1169-0.0180.11370.07820.0378-0.0306-00.3948-0.0005-0.05290.3406-0.03550.332920.3881104.428138.3546
61.9002-0.23250.62763.1118-0.7421.22-0.0568-0.2166-0.1330.04950.10030.12310.0652-0.11750.00010.40780.004-0.01710.40790.02720.371214.489882.87538.846
72.4256-0.6655-0.18682.1-0.87232.31260.03470.2427-0.1966-0.2446-0.0515-0.15150.2086-0.00040.00020.3899-0.01240.02170.3926-0.0050.374841.37675.432122.8288
80.1377-0.0185-0.1679-0.00040.01530.2023-0.42060.463-0.0865-0.624-0.1238-0.92720.050.6841-0.00311.12090.07970.16620.8438-0.23520.935248.287364.66292.1893
90.01470.09110.03080.1184-0.22690.37220.22850.29460.3575-0.7056-0.2867-1.71040.19770.4731-0.00081.31580.09320.49751.21060.08761.422752.737179.7148-8.138
102.3739-1.06340.39182.4858-0.04272.35270.02840.3520.2685-0.267-0.0667-0.1005-0.05190.09260.00010.3487-0.0077-0.00970.41840.06640.34929.626592.569816.0978
110.0271-0.01790.01380.0518-0.09840.2370.35430.73250.2924-1.4247-0.16060.0106-0.1765-0.07520.1521.49840.3470.35711.17840.5480.085634.057100.7422-6.3062
120.5836-0.53570.11910.3951-0.07690.19130.87561.01530.079-1.7946-0.5979-0.5346-0.0292-0.07350.00141.7390.20830.16021.28050.04410.695939.992587.3998-12.5788
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 1 through 119
2X-RAY DIFFRACTION2chain A and resi 120 through 125
3X-RAY DIFFRACTION3chain A and resi 126 through 230
4X-RAY DIFFRACTION4chain B and resi 1 through 105
5X-RAY DIFFRACTION5chain B and resi 106 through 113
6X-RAY DIFFRACTION6chain B and resi 114 through 214
7X-RAY DIFFRACTION7chain C and resi 1 through 119
8X-RAY DIFFRACTION8chain C and resi 120 through 125
9X-RAY DIFFRACTION9chain C and (resi 126 through 218)
10X-RAY DIFFRACTION10chain D and resi 1 through 105
11X-RAY DIFFRACTION11chain D and resi 106 through 113
12X-RAY DIFFRACTION12chain D and (resi 114 through 181)

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