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- PDB-6ck8: Crystal structure of anti-influenza single-domain llama antibody SD38 -

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Basic information

Entry
Database: PDB / ID: 6ck8
TitleCrystal structure of anti-influenza single-domain llama antibody SD38
ComponentsLlama antibody SD38
KeywordsIMMUNE SYSTEM / single-domain / multi-domain / llama / antibody / influenza / broad / neutralization
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsZhu, X. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI17675 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI27371 United States
CitationJournal: Science / Year: 2018
Title: Universal protection against influenza infection by a multidomain antibody to influenza hemagglutinin.
Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut ...Authors: Nick S Laursen / Robert H E Friesen / Xueyong Zhu / Mandy Jongeneelen / Sven Blokland / Jan Vermond / Alida van Eijgen / Chan Tang / Harry van Diepen / Galina Obmolova / Marijn van der Neut Kolfschoten / David Zuijdgeest / Roel Straetemans / Ryan M B Hoffman / Travis Nieusma / Jesper Pallesen / Hannah L Turner / Steffen M Bernard / Andrew B Ward / Jinquan Luo / Leo L M Poon / Anna P Tretiakova / James M Wilson / Maria P Limberis / Ronald Vogels / Boerries Brandenburg / Joost A Kolkman / Ian A Wilson /
Abstract: Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza ...Broadly neutralizing antibodies against highly variable pathogens have stimulated the design of vaccines and therapeutics. We report the use of diverse camelid single-domain antibodies to influenza virus hemagglutinin to generate multidomain antibodies with impressive breadth and potency. Multidomain antibody MD3606 protects mice against influenza A and B infection when administered intravenously or expressed locally from a recombinant adeno-associated virus vector. Crystal and single-particle electron microscopy structures of these antibodies with hemagglutinins from influenza A and B viruses reveal binding to highly conserved epitopes. Collectively, our findings demonstrate that multidomain antibodies targeting multiple epitopes exhibit enhanced virus cross-reactivity and potency. In combination with adeno-associated virus-mediated gene delivery, they may provide an effective strategy to prevent infection with influenza virus and other highly variable pathogens.
History
DepositionFeb 27, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Llama antibody SD38
B: Llama antibody SD38
C: Llama antibody SD38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,48526
Polymers40,2873
Non-polymers3,19723
Water2,918162
1
A: Llama antibody SD38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,71210
Polymers13,4291
Non-polymers1,2839
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Llama antibody SD38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,72010
Polymers13,4291
Non-polymers1,2919
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Llama antibody SD38
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0526
Polymers13,4291
Non-polymers6235
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.018, 75.267, 57.250
Angle α, β, γ (deg.)90.00, 92.62, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-303-

HOH

21A-345-

HOH

31A-348-

HOH

41A-353-

HOH

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Components

#1: Antibody Llama antibody SD38


Mass: 13429.163 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Homo sapiens (human) / Strain (production host): Expi293F cells
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 3.15 Å3/Da / Density % sol: 60.98 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.085 M HEPES, pH 8.5, 1.4 M ammonium sulfate, 1.7%(v/v) PEG400, 15% glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 25, 2014
RadiationMonochromator: Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 30303 / % possible obs: 96 % / Redundancy: 4.9 % / CC1/2: 1 / Rpim(I) all: 0.03 / Rsym value: 0.07 / Net I/σ(I): 27.3
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1084 / CC1/2: 0.95 / Rpim(I) all: 0.14 / Rsym value: 0.25 / % possible all: 70

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GRW

4grw


Resolution: 2.05→43.007 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.13
RfactorNum. reflection% reflection
Rfree0.2111 1523 5.03 %
Rwork0.1769 --
obs0.1786 30249 95.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→43.007 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2826 0 152 162 3140
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023009
X-RAY DIFFRACTIONf_angle_d0.6684050
X-RAY DIFFRACTIONf_dihedral_angle_d12.6891074
X-RAY DIFFRACTIONf_chiral_restr0.024432
X-RAY DIFFRACTIONf_plane_restr0.003501
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0499-2.1160.26461060.20962024X-RAY DIFFRACTION74
2.116-2.19160.22591240.21722363X-RAY DIFFRACTION88
2.1916-2.27940.24691280.21312579X-RAY DIFFRACTION95
2.2794-2.38310.25031410.21222681X-RAY DIFFRACTION99
2.3831-2.50870.26671570.20152704X-RAY DIFFRACTION100
2.5087-2.66590.21981620.20152656X-RAY DIFFRACTION100
2.6659-2.87170.24971370.19922762X-RAY DIFFRACTION100
2.8717-3.16060.23181430.18952692X-RAY DIFFRACTION100
3.1606-3.61780.20131270.17282743X-RAY DIFFRACTION100
3.6178-4.55720.15511470.14362742X-RAY DIFFRACTION100
4.5572-43.01650.221510.16682780X-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)
16.7713-0.2058-2.9823.35670.56926.65570.43360.14861.0259-0.2083-0.1126-0.1888-0.8001-0.068-0.31040.37290.0429-0.0240.3070.02460.3203-6.02612.237216.8123
24.7012-0.4132-3.79182.1315-0.89625.75640.3499-0.05770.25120.2081-0.09560.0499-0.58-0.4302-0.23360.34080.0291-0.0320.2576-0.00840.2641-13.2403-1.650227.2612
33.4324-0.417-3.33682.30810.72533.3196-0.02520.7419-0.1565-0.1874-0.27250.0953-0.0113-0.75560.35590.25470.0356-0.02340.3842-0.01560.3507-11.2236-7.385617.5516
41.39361.001-0.60374.1895-3.13572.4242-0.22060.8112-0.4773-0.84810.26090.23961.0405-1.5339-0.23920.4395-0.055-0.04040.5122-0.12340.3588-10.4753-10.456113.5794
55.40330.8036-1.47520.6662-0.71046.4611-0.12770.0002-0.36060.09520.0307-0.22080.54980.18050.12720.31110.0253-0.02260.2038-0.00490.3566-5.3259-11.499824.4918
65.29790.4426-1.17410.8353-2.11745.3174-0.02780.32190.061-0.1144-0.04310.0277-0.12610.57310.03110.2584-0.0034-0.0440.2191-0.0210.3264-2.5634-3.329720.5389
75.04282.6541-2.23111.3591-1.45372.9889-0.06050.6404-0.12580.00360.04110.19270.1979-1.0024-0.01110.2787-0.01050.00380.5351-0.05060.3068-20.9759-7.95620.8027
81.4463-0.69212.33825.608-0.80263.78920.06910.81320.3605-0.29460.019-0.228-0.3861-0.1459-0.08320.30780.09210.00980.42530.03340.3125-3.5830.909410.0269
92.13111.80961.76032.97773.21173.56950.21280.6964-0.6703-0.5970.3229-1.8831-0.38850.5791-0.3750.40590.0120.01660.33450.03870.5038-23.7377-1.260940.4768
102.75030.37590.74272.57583.95745.63-0.10190.1758-0.06030.26750.1003-0.00770.1234-0.076-0.0120.3157-0.01950.02670.29050.01070.3104-33.4654-6.958438.4801
114.8962.24040.61155.40112.03417.7577-0.01890.11210.5255-0.2984-0.26770.6203-0.3939-1.18160.13930.29340.04080.00040.3629-0.00120.4563-42.3146-2.734941.4262
122.44531.66380.08143.20790.54456.4179-0.12780.188-0.0429-0.11450.06380.12620.2738-0.41320.04430.259-0.00230.00040.3226-0.0120.3332-36.2353-9.735940.1268
136.98841.7031-1.34792.46390.6053.0501-0.3242.32871.0825-1.44680.09011.5778-1.868-0.90370.10741.13660.0448-0.23490.67350.03540.8306-34.357413.04343.4851
144.60730.4695-1.16283.38950.17674.0987-0.27340.452-0.12750.00940.3954-0.26680.1847-0.0688-0.14110.22290.0117-0.0090.3879-0.00780.2433-30.6132-7.297432.3665
153.74330.9791-0.4614.717-1.10934.80880.33890.0499-0.058-0.856-0.1571.3137-0.524-0.8153-0.21320.38650.1699-0.0240.444-0.02180.311-31.32217.264954.8368
161.19020.65170.68653.6171-0.99964.17650.177-0.4091-0.0794-0.1387-0.06110.18830.1248-0.1615-0.00050.31710.08490.00440.35780.01230.2987-24.556412.496264.99
171.7412-0.02590.94752.901-1.10325.03240.12040.3773-0.218-0.3933-0.28780.0762-0.42140.74550.10750.42860.11680.00810.44990.04090.367-20.351716.542855.2146
185.68330.13233.63323.13871.69753.27130.15850.8541-0.0977-1.2242-0.0411-0.33160.20640.69860.06490.62620.08370.08140.54070.03430.3869-17.976818.283951.1522
193.5146-2.84560.60165.8187-0.14555.46180.171-0.01690.5915-0.1329-0.0538-0.2963-0.7940.3654-0.13050.35370.00950.01910.24810.03120.3058-18.939223.709862.0983
202.3079-2.24620.17668.1094-1.78134.99740.1857-0.0333-0.1637-0.1524-0.05440.743-0.0632-0.2385-0.19590.26530.00890.01410.25460.04740.4459-28.093917.810964.9319
211.9805-1.1467-0.08590.6468-0.12820.9830.79190.7770.1674-0.8173-0.816-0.2543-0.73610.5122-0.04920.88660.2950.02810.4620.09090.3205-24.575221.883151.9117
224.817-1.17851.82940.77750.23696.02690.06250.1939-0.0346-0.1833-0.1242-0.08770.57421.1204-0.01910.48140.18250.01550.58260.05470.335-12.46014.8360.523
233.69471.3163-0.62281.29950.80211.32640.16050.68230.0754-0.6648-0.13081.0292-0.8069-0.5315-0.28960.7140.2782-0.10030.57720.05860.4241-31.294519.862747.9357
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:17 )A1 - 17
2X-RAY DIFFRACTION2( CHAIN A AND RESID 18:32 )A18 - 32
3X-RAY DIFFRACTION3( CHAIN A AND RESID 33:39 )A33 - 39
4X-RAY DIFFRACTION4( CHAIN A AND RESID 40:52 )A40 - 52
5X-RAY DIFFRACTION5( CHAIN A AND RESID 53:72 )A53 - 72
6X-RAY DIFFRACTION6( CHAIN A AND RESID 73:87 )A73 - 87
7X-RAY DIFFRACTION7( CHAIN A AND RESID 88:103 )A88 - 103
8X-RAY DIFFRACTION8( CHAIN A AND RESID 104:113 )A104 - 113
9X-RAY DIFFRACTION9( CHAIN B AND RESID 1:7 )B1 - 7
10X-RAY DIFFRACTION10( CHAIN B AND RESID 8:44 )B8 - 44
11X-RAY DIFFRACTION11( CHAIN B AND RESID 45:63 )B45 - 63
12X-RAY DIFFRACTION12( CHAIN B AND RESID 64:95 )B64 - 95
13X-RAY DIFFRACTION13( CHAIN B AND RESID 96:100 )B96 - 100
14X-RAY DIFFRACTION14( CHAIN B AND RESID 101:113 )B101 - 113
15X-RAY DIFFRACTION15( CHAIN C AND RESID 1:17 )C1 - 17
16X-RAY DIFFRACTION16( CHAIN C AND RESID 18:32 )C18 - 32
17X-RAY DIFFRACTION17( CHAIN C AND RESID 33:39 )C33 - 39
18X-RAY DIFFRACTION18( CHAIN C AND RESID 40:52 )C40 - 52
19X-RAY DIFFRACTION19( CHAIN C AND RESID 53:72 )C53 - 72
20X-RAY DIFFRACTION20( CHAIN C AND RESID 73:82 )C73 - 82
21X-RAY DIFFRACTION21( CHAIN C AND RESID 83:95 )C83 - 95
22X-RAY DIFFRACTION22( CHAIN C AND RESID 96:103 )C96 - 103
23X-RAY DIFFRACTION23( CHAIN C AND RESID 104:113 )C104 - 113

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