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- PDB-6o3l: Crystal structure of the Fab fragment of the human HIV-1 neutrali... -

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Basic information

Entry
Database: PDB / ID: 6o3l
TitleCrystal structure of the Fab fragment of the human HIV-1 neutralizing antibody PGZL1.H4K3 in complex with its MPER peptide epitope (region 671-683 of HIV-1 gp41).
Components
  • MPER peptide, region 671-683 of HIV-1 gp41
  • PGZL1.H4K3 heavy chain
  • PGZL1.H4K3 light chain
KeywordsIMMUNE SYSTEM / 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 / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / 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
PHOSPHATE ION / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHomo sapiens (human)
Human immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 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 26, 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.H4K3 light chain
H: PGZL1.H4K3 heavy chain
B: PGZL1.H4K3 light chain
A: PGZL1.H4K3 heavy chain
D: MPER peptide, region 671-683 of HIV-1 gp41
E: MPER peptide, region 671-683 of HIV-1 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,39917
Polymers99,3696
Non-polymers1,03011
Water8,611478
1
L: PGZL1.H4K3 light chain
H: PGZL1.H4K3 heavy chain
D: MPER peptide, region 671-683 of HIV-1 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,2469
Polymers49,6853
Non-polymers5616
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6140 Å2
ΔGint-53 kcal/mol
Surface area20700 Å2
MethodPISA
2
B: PGZL1.H4K3 light chain
A: PGZL1.H4K3 heavy chain
E: MPER peptide, region 671-683 of HIV-1 gp41
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,1548
Polymers49,6853
Non-polymers4695
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5830 Å2
ΔGint-50 kcal/mol
Surface area20530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.342, 58.029, 98.725
Angle α, β, γ (deg.)87.94, 76.09, 72.52
Int Tables number1
Space group name H-MP1

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Components

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Protein/peptide , 1 types, 2 molecules DE

#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 LBHA

#1: Antibody PGZL1.H4K3 light chain


Mass: 23276.662 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.H4K3 heavy chain


Mass: 24220.318 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, 489 molecules

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


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 478 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.95 Å3/Da / Density % sol: 58.33 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M ammonium dihydrogen phosphate, 22% PEG3350

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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: Mar 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.98→36.154 Å / Num. obs: 72569 / % possible obs: 91.3 % / Redundancy: 3.8 % / Biso Wilson estimate: 27 Å2 / CC1/2: 0.949 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.046 / Net I/σ(I): 12.6
Reflection shellResolution: 1.98→2.01 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 6 / Num. unique obs: 2807 / CC1/2: 0.977 / Rpim(I) all: 0.141 / % possible all: 70.7

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-20002.3.10data reduction
HKL-20002.3.10data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6O3K

6o3k


Resolution: 1.98→36.154 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 22.84
RfactorNum. reflection% reflection
Rfree0.2109 3617 4.99 %
Rwork0.1702 --
obs0.1722 72539 91.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 33 Å2
Refinement stepCycle: LAST / Resolution: 1.98→36.154 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6929 0 60 478 7467
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087351
X-RAY DIFFRACTIONf_angle_d0.92510040
X-RAY DIFFRACTIONf_dihedral_angle_d15.9854407
X-RAY DIFFRACTIONf_chiral_restr0.0581107
X-RAY DIFFRACTIONf_plane_restr0.0061283
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.00570.24631160.18982109X-RAY DIFFRACTION75
2.0057-2.03320.23541260.17952687X-RAY DIFFRACTION91
2.0332-2.06220.23931450.18242656X-RAY DIFFRACTION92
2.0622-2.0930.20161380.1812669X-RAY DIFFRACTION92
2.093-2.12570.28281500.17862667X-RAY DIFFRACTION92
2.1257-2.16060.23991330.17322659X-RAY DIFFRACTION92
2.1606-2.19780.24571190.17042677X-RAY DIFFRACTION92
2.1978-2.23780.21211490.16982639X-RAY DIFFRACTION90
2.2378-2.28080.22961430.17572520X-RAY DIFFRACTION89
2.2808-2.32740.26811250.18642496X-RAY DIFFRACTION85
2.3274-2.3780.26851370.18492708X-RAY DIFFRACTION95
2.378-2.43330.25771580.18612770X-RAY DIFFRACTION95
2.4333-2.49410.24871320.17822776X-RAY DIFFRACTION95
2.4941-2.56150.23181490.18162731X-RAY DIFFRACTION95
2.5615-2.63690.22071410.18722772X-RAY DIFFRACTION94
2.6369-2.7220.23841450.19052601X-RAY DIFFRACTION93
2.722-2.81920.2391400.18582588X-RAY DIFFRACTION89
2.8192-2.9320.23341400.1962736X-RAY DIFFRACTION94
2.932-3.06540.23031540.19672770X-RAY DIFFRACTION95
3.0654-3.22690.22651380.19252737X-RAY DIFFRACTION95
3.2269-3.4290.2261420.18412686X-RAY DIFFRACTION94
3.429-3.69350.20721340.16742539X-RAY DIFFRACTION88
3.6935-4.06470.19831420.15542745X-RAY DIFFRACTION95
4.0647-4.65180.1511460.12682727X-RAY DIFFRACTION94
4.6518-5.85680.14591360.13492585X-RAY DIFFRACTION89
5.8568-36.15980.1881390.17192672X-RAY DIFFRACTION92
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)
11.82460.80511.32552.24811.99211.99150.0936-0.18780.10870.3468-0.29320.18330.3909-0.330.23550.3005-0.01940.01260.1779-0.00760.2411-55.6817-33.4726-1.646
21.0079-0.35450.04811.24310.32032.48790.0241-0.0533-0.06890.2878-0.09220.06720.1485-0.08070.0520.2977-0.04250.00710.15990.01150.2123-48.8962-37.4326-7.0596
32.7143-1.5102-0.95823.08962.6684.3934-0.10680.002-0.28350.09830.04190.08240.5357-0.31980.08570.261-0.06620.00760.23440.04010.2076-55.1987-22.1318.2433
41.6456-0.1573-0.44073.0059-1.19232.48070.14060.15480.1585-0.1794-0.0240.1611-0.0954-0.3501-0.11760.1960.0165-0.00490.242-0.00650.1832-57.1432-4.77760.9094
50.6255-0.43980.78673.0821-1.33642.38180.21390.08370.29320.1021-0.06540.4399-0.4468-0.4781-0.16780.2560.15120.06840.29720.10950.355-62.94122.37821.2635
61.4222-0.416-0.09342.35110.26141.56870.0512-0.05150.0487-0.0087-0.1339-0.39980.04440.08960.10110.1902-0.0150.00860.2060.04860.204-35.2525-24.3056-23.3267
71.5459-0.7398-0.01553.67280.38114.12350.06910.18360.05170.0023-0.07490.07280.0999-0.22920.05990.2336-0.018-0.01760.17490.00130.1881-43.5197-29.787-25.4501
81.1998-0.14980.43172.14430.42842.22320.09570.1427-0.08160.0303-0.119-0.15120.15060.2087-0.01150.1954-0.00170.00270.21780.01240.1788-39.5435-29.4888-19.8804
91.6592-0.0096-0.22172.7323-0.06264.92830.0201-0.13430.0950.0271-0.0532-0.1481-0.10520.10050.02130.1761-0.02720.00370.17770.01910.2287-45.2352-2.2155-3.7038
102.01130.79510.03973.2619-0.16834.67060.087-0.32840.19760.3564-0.1095-0.2469-0.45190.3753-0.0220.3263-0.0637-0.04760.2584-0.00650.2935-41.16781.90561.514
111.81560.3429-1.56491.9989-0.98284.052-0.0710.0163-0.12790.0191-0.01680.147-0.1490.31280.0870.2573-0.075-0.04010.3022-0.04360.2455-53.875-19.07533.6958
121.49480.05480.12691.29410.31332.1127-0.0292-0.08310.0798-0.0323-0.01540.1852-0.0353-0.25410.02780.17710.0162-0.02560.2744-0.01660.2174-54.6182-9.54339.0932
131.87970.2225-0.49881.47510.45773.50140.05390.08820.0822-0.1178-0.02130.0473-0.1396-0.1123-0.04750.20360.0076-0.0150.3039-0.03060.2767-52.7958-12.61137.734
141.8515-1.6691-4.07521.50083.68248.9657-0.048-0.060.23330.07950.2599-0.01750.4364-0.3101-0.22630.2324-0.0494-0.03880.2979-0.01040.2491-45.3119-22.141521.512
152.86-0.57381.28632.37120.13433.1394-0.0329-0.1701-0.08350.25520.2751-0.3440.49370.4058-0.27260.33050.0756-0.04950.2814-0.0390.2233-25.6298-32.20923.143
164.086-2.1941.50113.7102-0.14932.7752-0.2269-0.3078-0.02060.41660.2947-0.01230.4002-0.1575-0.00530.2905-0.02590.00990.22570.01960.1465-32.899-29.43925.418
172.678-0.17090.82121.7089-0.0372.36540.07710.0643-0.49540.12560.1766-0.22340.72020.4031-0.24370.41810.1228-0.06830.279-0.03850.3004-24.2023-38.874921.2772
183.4472-1.32850.25172.6564-0.11172.2641-0.0289-0.03470.47580.0575-0.0525-0.1922-0.12040.11270.07310.2055-0.0403-0.030.2241-0.03270.2424-33.2375-4.09950.7753
194.0087-1.0316-0.22283.36021.03113.01760.0914-0.3036-0.24790.1148-0.17360.22110.2323-0.22510.15690.1393-0.0259-0.00940.2617-0.00910.1565-42.1666-11.190953.9303
204.2136-0.4053-0.04717.2453-0.00832.8162-0.0203-0.35360.42980.8270.0825-0.218-0.17950.20750.05720.2389-0.0144-0.04190.2847-0.07410.2254-35.0246-1.989757.2166
212.2697-0.109-0.35831.71150.28852.12290.11940.01390.3812-0.0832-0.176-0.0181-0.1696-0.17710.04340.192-0-0.00980.2438-0.03450.2022-41.5427-6.131347.4876
221.7455-0.2271-0.48281.5605-0.24871.0840.03830.2484-0.1289-0.15410.0755-0.11930.49470.5279-0.07790.29340.04240.00330.3991-0.04670.2954-17.3723-24.149329.589
231.20750.0120.5961.03650.02064.1108-0.02430.23610.1359-0.15070.1441-0.10220.03070.4962-0.07890.1633-0.01970.01210.3123-0.01330.2188-20.2301-19.168225.8068
244.108-0.8818-1.04144.75481.18944.07380.04830.3367-0.8868-0.0254-0.23560.1450.57410.29750.17070.45980.0493-0.04140.2291-0.03880.3515-38.2701-49.0957-25.6448
253.610.44520.67251.9395-0.3696.0711-0.17920.1504-0.14090.29250.04020.8451-0.3833-0.39020.1410.20220.03910.00820.3988-0.14230.3224-55.51664.595757.7935
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 102 )
3X-RAY DIFFRACTION3chain 'L' and (resid 103 through 113 )
4X-RAY DIFFRACTION4chain 'L' and (resid 114 through 174 )
5X-RAY DIFFRACTION5chain 'L' and (resid 175 through 213 )
6X-RAY DIFFRACTION6chain 'H' and (resid 1 through 33 )
7X-RAY DIFFRACTION7chain 'H' and (resid 33 through 75 )
8X-RAY DIFFRACTION8chain 'H' and (resid 76 through 111 )
9X-RAY DIFFRACTION9chain 'H' and (resid 112 through 184 )
10X-RAY DIFFRACTION10chain 'H' and (resid 486 through 526 )
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 18 )
12X-RAY DIFFRACTION12chain 'B' and (resid 19 through 69 )
13X-RAY DIFFRACTION13chain 'B' and (resid 70 through 101 )
14X-RAY DIFFRACTION14chain 'B' and (resid 102 through 113 )
15X-RAY DIFFRACTION15chain 'B' and (resid 114 through 150 )
16X-RAY DIFFRACTION16chain 'B' and (resid 151 through 174 )
17X-RAY DIFFRACTION17chain 'B' and (resid 175 through 213 )
18X-RAY DIFFRACTION18chain 'A' and (resid 1 through 32 )
19X-RAY DIFFRACTION19chain 'A' and (resid 33 through 66 )
20X-RAY DIFFRACTION20chain 'A' and (resid 67 through 82 )
21X-RAY DIFFRACTION21chain 'A' and (resid 83 through 111 )
22X-RAY DIFFRACTION22chain 'A' and (resid 112 through 136 )
23X-RAY DIFFRACTION23chain 'A' and (resid 137 through 229 )
24X-RAY DIFFRACTION24chain 'D' and (resid 671 through 686 )
25X-RAY DIFFRACTION25chain 'E' and (resid 671 through 686 )

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