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- PDB-6bla: Structure of AMM01 Fab, an anti EBV gH/gL neutralizing antibody -

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Basic information

Entry
Database: PDB / ID: 6bla
TitleStructure of AMM01 Fab, an anti EBV gH/gL neutralizing antibody
Components
  • AMM01 Fab Heavy chain
  • AMM01 Fab Light chain
KeywordsIMMUNE SYSTEM / SSGCID / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / antibody / Fab / EBV / gH/gL
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.55 Å
AuthorsPancera, M. / Weidle, C. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)
CitationJournal: Immunity / Year: 2018
Title: An Antibody Targeting the Fusion Machinery Neutralizes Dual-Tropic Infection and Defines a Site of Vulnerability on Epstein-Barr Virus.
Authors: Joost Snijder / Michael S Ortego / Connor Weidle / Andrew B Stuart / Matthew D Gray / M Juliana McElrath / Marie Pancera / David Veesler / Andrew T McGuire /
Abstract: Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and is associated with 200,000 new cases of cancer and 140,000 deaths annually. Subunit vaccines against this pathogen have ...Epstein-Barr virus (EBV) is a causative agent of infectious mononucleosis and is associated with 200,000 new cases of cancer and 140,000 deaths annually. Subunit vaccines against this pathogen have focused on the gp350 glycoprotein and remain unsuccessful. We isolated human antibodies recognizing the EBV fusion machinery (gH/gL and gB) from rare memory B cells. One anti-gH/gL antibody, AMMO1, potently neutralized infection of B cells and epithelial cells, the two major cell types targeted by EBV. We determined a cryo-electron microscopy reconstruction of the gH/gL-gp42-AMMO1 complex and demonstrated that AMMO1 bound to a discontinuous epitope formed by both gH and gL at the Domain-I/Domain-II interface. Integrating structural, biochemical, and infectivity data, we propose that AMMO1 inhibits fusion of the viral and cellular membranes. This work identifies a crucial epitope that may aid in the design of next-generation subunit vaccines against this major public health burden.
History
DepositionNov 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Other / Structure summary
Category: audit_author / pdbx_SG_project ...audit_author / pdbx_SG_project / pdbx_database_status / struct_keywords
Item: _pdbx_database_status.SG_entry / _struct_keywords.text

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: AMM01 Fab Heavy chain
L: AMM01 Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,04824
Polymers47,1932
Non-polymers1,85522
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-49 kcal/mol
Surface area21620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.893, 69.937, 136.313
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#1: Antibody AMM01 Fab Heavy chain


Mass: 24097.973 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 AMM01 Fab Light chain


Mass: 23095.514 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Non-polymers , 7 types, 367 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL / Polyethylene glycol


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 345 / 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: 2.52 Å3/Da / Density % sol: 51.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 16.75% PEG 400, 13.4% PEG 3350, 0.1M MgCl2, 0.1M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Nov 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→50 Å / Num. obs: 61916 / % possible obs: 88.3 % / Redundancy: 5.7 % / Net I/σ(I): 9.1

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementResolution: 1.55→48.811 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1937 3104 5.02 %
Rwork0.166 --
obs0.1674 61849 88.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.55→48.811 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3303 0 99 345 3747
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093480
X-RAY DIFFRACTIONf_angle_d1.0064721
X-RAY DIFFRACTIONf_dihedral_angle_d11.8742061
X-RAY DIFFRACTIONf_chiral_restr0.063524
X-RAY DIFFRACTIONf_plane_restr0.007599
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5497-1.57390.3216470.2756893X-RAY DIFFRACTION30
1.5739-1.59970.2807740.26241315X-RAY DIFFRACTION44
1.5997-1.62730.2715750.23191656X-RAY DIFFRACTION55
1.6273-1.65690.22611120.21961964X-RAY DIFFRACTION66
1.6569-1.68870.22031160.2212317X-RAY DIFFRACTION77
1.6887-1.72320.23911420.2392667X-RAY DIFFRACTION89
1.7232-1.76070.22431550.20692838X-RAY DIFFRACTION96
1.7607-1.80160.21391740.18772863X-RAY DIFFRACTION97
1.8016-1.84670.21461430.17992934X-RAY DIFFRACTION96
1.8467-1.89660.18381590.17312908X-RAY DIFFRACTION98
1.8966-1.95240.18721540.16222949X-RAY DIFFRACTION98
1.9524-2.01540.19191720.15792919X-RAY DIFFRACTION98
2.0154-2.08750.17151530.15842956X-RAY DIFFRACTION98
2.0875-2.17110.20481480.15432987X-RAY DIFFRACTION99
2.1711-2.26990.16921430.16433021X-RAY DIFFRACTION99
2.2699-2.38950.22541780.15922977X-RAY DIFFRACTION99
2.3895-2.53920.18931530.16033014X-RAY DIFFRACTION99
2.5392-2.73530.19611590.16343043X-RAY DIFFRACTION100
2.7353-3.01050.18451470.16693052X-RAY DIFFRACTION100
3.0105-3.4460.191510.17023100X-RAY DIFFRACTION100
3.446-4.34120.18721720.15673107X-RAY DIFFRACTION100
4.3412-48.83550.1931770.16493265X-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)
11.07910.2856-0.310.8245-0.42853.18310.03090.0144-0.0327-0.05160.00130.03490.1623-0.0704-0.03850.23550.01340.00560.23230.01270.280618.070818.19136.9419
21.8915-0.4537-1.13511.50910.45583.33740.0835-0.06650.05040.00340.004-0.1431-0.17960.1985-0.04220.2063-0.0131-0.01210.24220.00560.26327.247223.0411141.4932
30.723-0.3534-0.75450.6341-0.61192.60960.01410.01440.04750.0101-0.0659-0.119-0.01240.13790.0670.2076-0.0101-0.01350.2274-0.00250.272620.366519.9226141.413
44.1449-1.3665-0.81113.2974-0.97524.6538-0.1074-0.30880.43640.65790.07910.197-0.4579-0.2415-0.22580.3855-0.010.01570.2966-0.02640.3361-4.816129.285177.9077
53.856-2.0987-1.33553.54391.20112.06460.03080.01440.06590.0058-0.02880.1096-0.0585-0.1094-0.01050.274-0.0043-0.01380.25950.01470.24-4.199522.4182166.1302
62.68910.67111.99551.65631.96593.10530.1339-0.1765-0.0727-0.0857-0.49990.3845-0.0214-0.58110.39390.3252-0.04980.04090.28110.01060.2824-6.640718.5407175.1107
76.479-2.2932-0.72612.354-0.14591.3414-0.0643-0.1595-0.03180.28950.04810.0171-0.1929-0.02550.04140.3064-0.0212-0.01540.1749-0.01510.244215.015945.6361147.6128
82.2238-0.2238-0.10141.6256-0.36871.121-0.0309-0.00980.00880.02780.0057-0.0999-0.1143-0.01130.02650.24280.0020.00070.20810.00780.230817.333742.2352138.8581
94.1067-2.43-1.83163.20070.31372.2074-0.1178-0.06050.0430.0049-0.01-0.43650.05430.21370.09870.1992-0.0155-0.01640.1902-0.00770.285323.316535.848144.5951
10-0.03040.02130.13421.6667-1.4332.3802-0.0247-0.05450.0090.21490.0312-0.0257-0.1312-0.0953-0.030.29450.00850.01810.26340.00010.28714.373133.1332168.6413
112.2124-1.76223.12624.0611-2.61847.5810.098-0.07060.01-0.0671-0.0831-0.17320.19320.0521-0.0540.2296-0.02290.0490.2385-0.00740.27668.788230.835167.8935
122.2115-1.8782.68036.16-3.7656.95480.0692-0.0860.12940.40480.0429-0.1633-0.1351-0.10490.23770.2734-0.0107-0.00150.2297-0.03410.28888.759838.2304174.8095
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'H' and (resid 40 through 66 )
3X-RAY DIFFRACTION3chain 'H' and (resid 67 through 125 )
4X-RAY DIFFRACTION4chain 'H' and (resid 126 through 140 )
5X-RAY DIFFRACTION5chain 'H' and (resid 141 through 209 )
6X-RAY DIFFRACTION6chain 'H' and (resid 210 through 222 )
7X-RAY DIFFRACTION7chain 'L' and (resid 2 through 17 )
8X-RAY DIFFRACTION8chain 'L' and (resid 18 through 91 )
9X-RAY DIFFRACTION9chain 'L' and (resid 92 through 110 )
10X-RAY DIFFRACTION10chain 'L' and (resid 111 through 154 )
11X-RAY DIFFRACTION11chain 'L' and (resid 155 through 191 )
12X-RAY DIFFRACTION12chain 'L' and (resid 192 through 216 )

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