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- PDB-6o42: Crystal structure of the germline PGZL1 (PGZL1_gVmDmJ) Fab in com... -

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Basic information

Entry
Database: PDB / ID: 6o42
TitleCrystal structure of the germline PGZL1 (PGZL1_gVmDmJ) Fab in complex with MPER peptide epitope.
Components
  • (PGZL1_gVmDmJ ...) x 2
  • MPER peptide, region 671-683 of HIV-1 gp41
KeywordsIMMUNE SYSTEM / germline PGZL1 ANTI HIV-1 / GP41 MPER / MEMBRANE LIPIDS / BROADLY NEUTRALISING HIV-1 ANTIBODY
Function / homology
Function and homology information


Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane ...Synthesis and processing of ENV and VPU / evasion of host immune response / Alpha-defensins / Dectin-2 family / Binding and entry of HIV virion / positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / positive regulation of establishment of T cell polarity / virus-mediated perturbation of host defense response / host cell endosome membrane / actin filament organization / Assembly Of The HIV Virion / Budding and maturation of HIV virion / clathrin-dependent endocytosis of virus by host cell / viral protein processing / symbiont entry into host cell / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / structural molecule activity / virion attachment to host cell / host cell plasma membrane / virion membrane / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsIrimia, A. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
CitationJournal: Nat Commun / Year: 2019
Title: An MPER antibody neutralizes HIV-1 using germline features shared among donors.
Authors: Lei Zhang / Adriana Irimia / Lingling He / Elise Landais / Kimmo Rantalainen / Daniel P Leaman / Thomas Vollbrecht / Armando Stano / Daniel I Sands / Arthur S Kim / / Pascal Poignard / ...Authors: Lei Zhang / Adriana Irimia / Lingling He / Elise Landais / Kimmo Rantalainen / Daniel P Leaman / Thomas Vollbrecht / Armando Stano / Daniel I Sands / Arthur S Kim / / Pascal Poignard / Dennis R Burton / Ben Murrell / Andrew B Ward / Jiang Zhu / Ian A Wilson / Michael B Zwick /
Abstract: The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic ...The membrane-proximal external region (MPER) of HIV-1 envelope glycoprotein (Env) can be targeted by neutralizing antibodies of exceptional breadth. MPER antibodies usually have long, hydrophobic CDRH3s, lack activity as inferred germline precursors, are often from the minor IgG3 subclass, and some are polyreactive, such as 4E10. Here we describe an MPER broadly neutralizing antibody from the major IgG1 subclass, PGZL1, which shares germline V/D-region genes with 4E10, has a shorter CDRH3, and is less polyreactive. A recombinant sublineage variant pan-neutralizes a 130-isolate panel at 1.4 μg/ml (IC). Notably, a germline revertant with mature CDR3s neutralizes 12% of viruses and still binds MPER after DJ reversion. Crystal structures of lipid-bound PGZL1 variants and cryo-EM reconstruction of an Env-PGZL1 complex reveal how these antibodies recognize MPER and viral membrane. Discovery of common genetic and structural elements among MPER antibodies from different patients suggests that such antibodies could be elicited using carefully designed immunogens.
History
DepositionFeb 27, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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
L: PGZL1_gVmDmJ light chain
H: PGZL1_gVmDmJ heavy chain
A: PGZL1_gVmDmJ light chain
B: PGZL1_gVmDmJ heavy chain
G: MPER peptide, region 671-683 of HIV-1 gp41
I: MPER peptide, region 671-683 of HIV-1 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,58911
Polymers99,1256
Non-polymers4645
Water1,27971
1
L: PGZL1_gVmDmJ light chain
H: PGZL1_gVmDmJ heavy chain
G: MPER peptide, region 671-683 of HIV-1 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9357
Polymers49,5623
Non-polymers3724
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-33 kcal/mol
Surface area20060 Å2
MethodPISA
2
A: PGZL1_gVmDmJ light chain
B: PGZL1_gVmDmJ heavy chain
I: MPER peptide, region 671-683 of HIV-1 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6554
Polymers49,5623
Non-polymers921
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-50 kcal/mol
Surface area20430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)208.360, 37.920, 133.520
Angle α, β, γ (deg.)90.00, 93.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein/peptide , 1 types, 2 molecules GI

#3: Protein/peptide MPER peptide, region 671-683 of HIV-1 gp41


Mass: 2187.582 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Human immunodeficiency virus 1 / References: UniProt: P04578*PLUS

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Antibody , 2 types, 4 molecules LAHB

#1: Antibody PGZL1_gVmDmJ light chain


Mass: 23434.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi 293F / Production host: Homo sapiens (human)
#2: Antibody PGZL1_gVmDmJ heavy chain


Mass: 23939.955 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): Expi 293F / Production host: Homo sapiens (human)

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Non-polymers , 3 types, 76 molecules

#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.71 Å3/Da / Density % sol: 54.2 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1 M sodium acetate pH 4.6, 0.2 M ammonium sulfate, 30% PEG 2000 monomethyl ether, 8 MM 06:0 PA

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.6→39.77 Å / Num. obs: 30972 / % possible obs: 93.8 % / Redundancy: 2.9 % / Biso Wilson estimate: 43 Å2 / CC1/2: 0.987 / Rpim(I) all: 0.107 / Rsym value: 0.153 / Net I/σ(I): 6.4
Reflection shellResolution: 2.6→2.67 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 1.2 / Num. unique obs: 2317 / CC1/2: 0.571 / Rpim(I) all: 0.731 / Rsym value: 0.984 / % possible all: 95.2

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDS20180319data reduction
XSCALE20180319data scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O41

6o41


Resolution: 2.6→39.766 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 37.69
RfactorNum. reflection% reflection
Rfree0.31 1545 4.99 %
Rwork0.2566 --
obs0.2593 30948 93.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 49 Å2
Refinement stepCycle: LAST / Resolution: 2.6→39.766 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6821 0 29 71 6921
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0027109
X-RAY DIFFRACTIONf_angle_d0.5369689
X-RAY DIFFRACTIONf_dihedral_angle_d15.1314257
X-RAY DIFFRACTIONf_chiral_restr0.0421077
X-RAY DIFFRACTIONf_plane_restr0.0041236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5999-2.68380.46081420.39362669X-RAY DIFFRACTION95
2.6838-2.77970.46951390.34282676X-RAY DIFFRACTION95
2.7797-2.8910.4241390.32982737X-RAY DIFFRACTION96
2.891-3.02250.35191350.30152671X-RAY DIFFRACTION96
3.0225-3.18180.35771510.30692711X-RAY DIFFRACTION96
3.1818-3.38110.35781380.28732653X-RAY DIFFRACTION94
3.3811-3.6420.32761330.2762569X-RAY DIFFRACTION91
3.642-4.00820.30491450.24542664X-RAY DIFFRACTION94
4.0082-4.58740.261430.20622702X-RAY DIFFRACTION94
4.5874-5.77680.22781320.20392609X-RAY DIFFRACTION90
5.7768-39.77020.24911480.21672742X-RAY DIFFRACTION91
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)
11.5072-0.73060.69132.9187-0.09761.351-0.1980.19140.2117-0.2706-0.07290.0597-0.405-0.5928-0.02490.4655-0.0008-0.07230.3678-0.05390.1227-54.372121.881830.8055
21.71211.5223-1.53859.973-5.29873.9864-0.195-0.0085-0.2066-0.45090.41090.71230.4416-0.1631-0.24360.5926-0.0258-0.08310.3913-0.01940.3231-52.411517.533840.5424
31.1308-0.94330.22544.2432-0.91135.6381-0.3558-0.0470.3912-0.00980.07040.6116-0.81550.11370.29580.55-0.0563-0.05760.2851-0.06830.3747-45.380428.205840.9847
41.5506-1.0492-0.45432.5094-2.20513.6592-0.05690.1444-0.08540.279-0.16420.0874-0.148-0.1271-0.23310.52110.0148-0.18080.4015-0.0020.1942-50.589322.065937.5664
50.2001-0.11670.10740.252-0.60871.69150.0762-0.0098-0.0503-0.0248-0.0009-0.01970.1551-0.03120.29470.41060.0849-0.10410.3427-0.04890.1263-50.380730.897217.168
61.9071-0.95850.77592.55420.83584.3329-0.13370.1697-0.0276-0.26210.01050.276-0.21490.36360.08610.5162-0.0074-0.17160.2167-0.00440.1942-27.290222.1369-1.5234
71.73920.263-1.38712.064-0.05911.752-0.04960.0226-0.2838-0.11930.0728-0.06680.2767-0.15350.0650.31810.043-0.09560.18950.10540.2115-41.840722.48655.0327
81.9459-1.0430.49140.5807-0.45291.95-0.0825-0.28380.04980.02770.1288-0.0275-0.24520.14460.39890.5312-0.1194-0.2210.32840.11340.3092-41.15322.57239.1813
92.2155-0.3231.49992.00880.24371.77430.02880.49250.09980.0987-0.37920.25830.1315-0.21130.35110.6217-0.0379-0.26220.4196-0.04890.3877-35.316116.6023-4.0302
100.00060.00330.01940.18060.491.44770.22260.2410.0513-0.1412-0.2618-0.0385-0.0945-0.201-0.54040.51950.0017-0.12860.4180.14330.2164-43.25525.4298-4.2106
111.30850.3363-0.08420.5465-0.59711.59-0.0227-0.22060.16210.044-0.1746-0.1536-0.08270.1236-0.38770.2958-0.0072-0.12420.29280.0390.1008-24.736913.093734.8987
123.78350.7865-0.24811.8257-0.2864.6833-0.1147-0.26910.11150.1579-0.2209-0.12880.03360.27710.24260.50670.0229-0.10430.26380.0550.1859-33.566311.643543.5915
133.60790.4367-0.47152.3080.00583.5317-0.2198-0.3343-0.00210.5015-0.1047-0.09380.18630.59450.1990.5257-0.0263-0.06850.35120.12010.2963-32.018513.365141.6256
142.1764-0.1145-0.13153.6755-0.03081.79110.24430.0912-0.07730.0716-0.14880.1027-0.12810.1016-0.09380.4705-0.0067-0.06780.2850.0210.1329-25.266925.841110.5311
153.16670.547-0.23792.23210.64682.4268-0.23360.32990.3028-0.24370.07080.1457-0.05170.1447-0.04650.33080.0377-0.09660.3585-0.00950.0918-72.93116.940634.6762
164.35081.5149-0.40883.3442-2.12441.43440.0482-0.13740.5320.2939-0.05290.393-0.14520.1115-0.11770.38980.0162-0.02610.302-0.06470.2091-70.455621.574344.0412
173.4776-0.5921-0.08063.9118-0.55283.7990.20210.1547-0.88510.2520.2353-0.10670.5160.0628-0.36310.44390.03-0.11790.4012-0.06610.2145-73.461612.477645.9488
183.2450.12580.66372.19421.63524.94610.47110.0041-0.35980.5485-0.1228-0.2960.6570.01-0.22910.5379-0.0052-0.11070.3556-0.10070.1896-77.262810.903339.8831
192.8106-1.44860.10451.2373-1.42755.3227-0.186-0.17940.33320.2047-0.0811-0.2562-0.47050.13320.06370.5288-0.0479-0.14830.33280.04150.173-75.899226.724446.4981
200.42360.450.69440.97051.27441.726-0.01530.3137-0.1065-0.12820.00660.1267-0.02480.1424-0.35620.54180.0654-0.15310.3118-0.07270.1824-81.83847.825124.0317
211.6837-0.10171.45371.793-1.27942.05050.12860.16750.05270.0765-0.2317-0.2136-0.0243-0.3443-0.45520.62770.0477-0.21680.49870.05530.2348-110.010215.991816.5628
223.31640.4743-0.78430.7392-1.02441.930.01810.07870.52990.01760.43690.0173-0.25210.1570.59450.6507-0.101-0.14090.3435-0.020.3258-96.203417.149315.6842
231.5952-1.35150.0622.4865-1.08061.6767-0.0795-0.55030.296-0.00750.0182-0.11490.1024-0.03330.01850.5109-0.1182-0.05970.3298-0.11710.2173-92.859815.294922.5843
242.71721.0534-0.22930.4091-0.08042.7481-0.11860.34420.4449-0.2777-0.0160.1414-0.3868-0.12040.03930.59220.0418-0.09220.2616-0.0150.1815-103.497421.374711.4818
254.281-1.25610.42072.99860.23680.6136-0.11990.04750.0579-0.2991-0.13010.4173-0.1062-0.03570.140.60740.0006-0.1870.5405-0.01550.2047-98.157113.29267.3472
260.76220.57610.57871.22080.52113.4563-0.2555-0.20970.07180.21210.15160.1291-0.2648-0.232-0.0720.4628-0.0008-0.00540.45330.04950.1231-94.554423.276256.2138
272.9443-0.1155-1.38441.33470.75672.52410.0696-0.25430.4435-0.0622-0.0786-0.1124-0.5131-0.33270.32220.61260.0278-0.19490.37280.02560.2827-86.317230.383253.0851
282.5433-0.42690.40390.97311.81554.2754-0.28390.29570.06140.1445-0.08890.124-0.5898-0.2680.10850.6085-0.0519-0.06980.3213-0.10380.1887-92.700928.196652.0792
290.9778-0.27650.82050.43750.47962.0972-0.0002-0.3094-0.04270.2161-0.02660.02020.2571-0.0839-0.23970.5799-0.0375-0.08180.5527-0.07010.1485-75.411214.374361.9326
302.12580.22592.46471.58360.712.97310.0962-0.2348-0.07630.1026-0.18420.05370.1827-0.26960.2110.3912-0.01490.130.33470.01990.2753-101.09118.982937.1007
311.51540.12910.73931.77080.98271.6058-0.0733-0.05590.1648-0.0084-0.12410.1016-0.12420.17120.11520.4215-0.004-0.18290.37250.07410.2316-106.612815.143930.3373
322.8525-0.21850.11950.08620.4262.74410.2676-0.0412-0.4165-0.60550.16620.60070.4428-0.33880.06640.6399-0.0023-0.30750.37360.10420.4388-104.45698.922226.5027
331.10340.32491.37883.48942.48734.13190.0153-0.2807-0.01070.22330.29020.13280.9206-0.0955-0.41880.3733-0.0382-0.1260.41190.09110.2963-113.488210.977229.5895
345.1327-1.60191.03345.2725-2.91074.0272-0.2623-0.97560.70641.33350.41440.1875-0.4497-0.06210.11170.92230.0809-0.04130.51020.02420.387-40.759614.799759.3714
354.70892.0627-0.50574.06482.46859.8591-0.4749-0.9579-0.07351.09920.027-1.47180.33041.0976-0.02460.78210.0503-0.32070.6633-0.08990.7249-73.412223.998666.3787
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 18 )
2X-RAY DIFFRACTION2chain 'L' and (resid 19 through 38 )
3X-RAY DIFFRACTION3chain 'L' and (resid 39 through 61 )
4X-RAY DIFFRACTION4chain 'L' and (resid 62 through 102 )
5X-RAY DIFFRACTION5chain 'L' and (resid 103 through 113 )
6X-RAY DIFFRACTION6chain 'L' and (resid 114 through 128 )
7X-RAY DIFFRACTION7chain 'L' and (resid 129 through 150 )
8X-RAY DIFFRACTION8chain 'L' and (resid 151 through 174 )
9X-RAY DIFFRACTION9chain 'L' and (resid 175 through 197 )
10X-RAY DIFFRACTION10chain 'L' and (resid 198 through 213 )
11X-RAY DIFFRACTION11chain 'H' and (resid 1 through 17 )
12X-RAY DIFFRACTION12chain 'H' and (resid 18 through 63 )
13X-RAY DIFFRACTION13chain 'H' and (resid 64 through 111 )
14X-RAY DIFFRACTION14chain 'H' and (resid 112 through 228 )
15X-RAY DIFFRACTION15chain 'A' and (resid 1 through 18 )
16X-RAY DIFFRACTION16chain 'A' and (resid 19 through 38 )
17X-RAY DIFFRACTION17chain 'A' and (resid 39 through 75 )
18X-RAY DIFFRACTION18chain 'A' and (resid 76 through 90 )
19X-RAY DIFFRACTION19chain 'A' and (resid 91 through 102 )
20X-RAY DIFFRACTION20chain 'A' and (resid 103 through 113 )
21X-RAY DIFFRACTION21chain 'A' and (resid 114 through 128 )
22X-RAY DIFFRACTION22chain 'A' and (resid 129 through 152 )
23X-RAY DIFFRACTION23chain 'A' and (resid 153 through 174 )
24X-RAY DIFFRACTION24chain 'A' and (resid 175 through 198 )
25X-RAY DIFFRACTION25chain 'A' and (resid 199 through 213 )
26X-RAY DIFFRACTION26chain 'B' and (resid 1 through 32 )
27X-RAY DIFFRACTION27chain 'B' and (resid 33 through 72 )
28X-RAY DIFFRACTION28chain 'B' and (resid 73 through 95 )
29X-RAY DIFFRACTION29chain 'B' and (resid 96 through 100F )
30X-RAY DIFFRACTION30chain 'B' and (resid 100G through 137 )
31X-RAY DIFFRACTION31chain 'B' and (resid 138 through 157 )
32X-RAY DIFFRACTION32chain 'B' and (resid 162 through 206 )
33X-RAY DIFFRACTION33chain 'B' and (resid 207 through 230 )
34X-RAY DIFFRACTION34chain 'G' and (resid 671 through 685 )
35X-RAY DIFFRACTION35chain 'I' and (resid 671 through 685 )

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