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- PDB-5feh: Crystal structure of PCT64_35B, a broadly neutralizing anti-HIV a... -

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Basic information

Entry
Database: PDB / ID: 5feh
TitleCrystal structure of PCT64_35B, a broadly neutralizing anti-HIV antibody
Components
  • PCT64_26 Fab heavy chain
  • PCT64_26 Fab light chain
KeywordsIMMUNE SYSTEM / HIV / broadly neutralizing antibody / V1/V2
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsMurrell, S. / Wilson, I.A.
CitationJournal: Immunity / Year: 2017
Title: HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage.
Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de ...Authors: Elise Landais / Ben Murrell / Bryan Briney / Sasha Murrell / Kimmo Rantalainen / Zachary T Berndsen / Alejandra Ramos / Lalinda Wickramasinghe / Melissa Laird Smith / Kemal Eren / Natalia de Val / Mengyu Wu / Audrey Cappelletti / Jeffrey Umotoy / Yolanda Lie / Terri Wrin / Paul Algate / Po-Ying Chan-Hui / Etienne Karita / / / Andrew B Ward / Ian A Wilson / Dennis R Burton / Davey Smith / Sergei L Kosakovsky Pond / Pascal Poignard /
Abstract: Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb ...Understanding how broadly neutralizing antibodies (bnAbs) to HIV envelope (Env) develop during natural infection can help guide the rational design of an HIV vaccine. Here, we described a bnAb lineage targeting the Env V2 apex and the Ab-Env co-evolution that led to development of neutralization breadth. The lineage Abs bore an anionic heavy chain complementarity-determining region 3 (CDRH3) of 25 amino acids, among the shortest known for this class of Abs, and achieved breadth with only 10% nucleotide somatic hypermutation and no insertions or deletions. The data suggested a role for Env glycoform heterogeneity in the activation of the lineage germline B cell. Finally, we showed that localized diversity at key V2 epitope residues drove bnAb maturation toward breadth, mirroring the Env evolution pattern described for another donor who developed V2-apex targeting bnAbs. Overall, these findings suggest potential strategies for vaccine approaches based on germline-targeting and serial immunogen design.
History
DepositionDec 17, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Sep 27, 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
Revision 1.3Oct 23, 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: PCT64_26 Fab light chain
B: PCT64_26 Fab heavy chain
C: PCT64_26 Fab light chain
D: PCT64_26 Fab heavy chain
E: PCT64_26 Fab light chain
F: PCT64_26 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,0048
Polymers149,8466
Non-polymers1582
Water543
1
A: PCT64_26 Fab light chain
B: PCT64_26 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0453
Polymers49,9492
Non-polymers961
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3430 Å2
ΔGint-32 kcal/mol
Surface area19490 Å2
MethodPISA
2
C: PCT64_26 Fab light chain
D: PCT64_26 Fab heavy chain


Theoretical massNumber of molelcules
Total (without water)49,9492
Polymers49,9492
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3250 Å2
ΔGint-23 kcal/mol
Surface area20210 Å2
MethodPISA
3
E: PCT64_26 Fab light chain
F: PCT64_26 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0113
Polymers49,9492
Non-polymers621
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-24 kcal/mol
Surface area21030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)135.525, 135.525, 353.602
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody PCT64_26 Fab light chain


Mass: 23549.037 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCT64_26 Fab heavy chain


Mass: 26399.561 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: 3.13 Å3/Da / Density % sol: 60.68 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: ammonium sulfate, ethylene glycol, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 3.1→48.892 Å / Num. obs: 35800 / % possible obs: 99.4 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.8
Reflection shellResolution: 3.1→3.17 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.9 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.10_2155refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFB

1dfb


Resolution: 3.1→48.892 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.279 1810 5.07 %
Rwork0.2592 --
obs0.2602 35719 99.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.1→48.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9667 0 9 3 9679
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0049902
X-RAY DIFFRACTIONf_angle_d0.76513453
X-RAY DIFFRACTIONf_dihedral_angle_d14.4233604
X-RAY DIFFRACTIONf_chiral_restr0.0471503
X-RAY DIFFRACTIONf_plane_restr0.0051721
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1-3.17970.36641280.34642527X-RAY DIFFRACTION99
3.1797-3.27330.34721720.33792521X-RAY DIFFRACTION100
3.2733-3.37890.3471550.31642548X-RAY DIFFRACTION100
3.3789-3.49960.29261200.29412580X-RAY DIFFRACTION100
3.4996-3.63970.30561430.28122524X-RAY DIFFRACTION98
3.6397-3.80530.2791110.28022613X-RAY DIFFRACTION100
3.8053-4.00580.24991450.27242584X-RAY DIFFRACTION100
4.0058-4.25670.31741480.25132593X-RAY DIFFRACTION100
4.2567-4.58510.24131410.21532591X-RAY DIFFRACTION100
4.5851-5.04610.26071310.21162607X-RAY DIFFRACTION99
5.0461-5.77530.24581420.22982639X-RAY DIFFRACTION100
5.7753-7.27240.26191390.26282682X-RAY DIFFRACTION99
7.2724-48.89780.24391350.23572900X-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)
10.38160.1097-0.04830.2164-0.00620.3422-0.05540.1393-0.0663-0.2044-0.0787-0.08130.12690.19060.07770.60630.2465-0.12290.4585-0.00150.5511-36.3504-53.8113-33.0476
20.2607-0.06370.02760.25820.05890.52840.1279-0.0219-0.44880.08460.12910.15160.49460.0974-0.19750.8420.2197-0.1780.3727-0.0790.71-37.7663-65.206-33.4253
30.95380.1414-0.64920.0258-0.05851.03330.07450.3484-0.0543-0.0979-0.02550.04670.10160.12650.00090.69920.3026-0.2310.4031-0.10980.4954-40.2439-60.7036-39.0942
40.46430.29930.15010.3547-0.2240.58020.09820.3155-0.3519-0.2320.130.23170.50330.1357-0.13350.75760.4802-0.07190.48560.03380.3905-35.5842-61.8146-31.0442
51.4206-1.61850.27274.2566-0.06381.2657-0.0597-0.00210.02540.23040.1142-0.09540.01310.0685-0.01940.61960.2692-0.01610.29790.0530.3284-39.5214-44.215-20.5066
66.45991.41621.56923.49690.87436.40040.18970.23040.41590.5334-0.1455-0.77280.01080.8693-0.03050.33430.1785-0.07950.36740.03690.6921-21.7973-39.2574-9.5097
77.35456.45530.31496.22271.97785.2019-0.11890.54891.3726-0.18230.3214-0.6188-0.25230.879-0.27150.44370.1240.18490.72290.17871.0493-15.3893-37.1634-16.2757
81.92081.54191.43535.923-0.45555.0810.02380.64960.4020.33880.0085-0.9646-0.25970.9473-0.04680.39970.16290.00780.38490.04320.6852-21.6249-39.2575-11.549
92.00470.02357.35668.51160.94886.7849-0.8501-0.05532.20820.2760.2039-0.9567-1.0660.43130.77330.41030.10060.10840.61950.11240.8837-23.9893-29.2335-11.0462
108.36271.63522.70411.1937-0.57282.50520.2705-0.1473-1.8165-0.8024-0.00060.01791.1969-0.0639-0.32721.13020.5933-0.12250.80940.10920.7479-22.5719-73.6017-20.0204
111.3317-0.61340.16410.3319-0.23960.76890.01470.3078-1.365-0.7562-0.22810.61741.13350.1469-0.23251.05781.8006-0.8070.01740.77850.3378-19.6747-72.6633-22.642
126.98783.7482-3.27485.3371.43454.60220.12671.16831.365-0.8272-0.40770.9228-0.8407-0.55290.2380.87370.1415-0.21240.84890.20230.5129-25.7734-38.2408-0.1896
133.015-0.55040.36413.6925-1.17231.507-0.0973-0.43190.33170.99320.0692-0.1506-0.16140.44750.02010.51530.4204-0.04870.49350.03850.3861-24.3532-50.1022-0.487
140.5870.11740.14340.6448-0.2670.19450.2386-0.0291-0.0197-0.0230.23180.96450.1202-0.692-0.23640.6283-0.3064-0.1580.99940.24710.8979-20.8102-103.879715.6973
151.11410.14960.01160.74430.05760.70580.026-0.0312-0.1759-0.14110.24530.76880.518-0.6956-0.14070.4062-0.1424-0.20330.56640.23130.7121-13.8317-100.468213.1903
161.63580.03210.07934.96150.33182.6805-0.11380.23080.51340.03440.15540.0812-0.39140.0067-0.04360.22890.0656-0.07920.16850.09860.33547.9259-80.79910.8916
175.56593.81320.2915.01222.88976.59960.6139-0.54970.59221.22630.0922-0.2989-0.49910.336-0.56990.8372-0.0735-0.11940.26010.07490.56166.3064-77.357420.1533
183.63081.82780.45776.98040.58083.1634-0.04450.50560.3177-0.05930.1096-0.0556-0.12240.2216-0.08120.1987-0.0101-0.08050.20360.05580.25669.9674-82.127513.4948
190.54920.1035-0.25050.382-0.28180.22320.2754-0.1067-0.1233-0.27040.13691.03150.3396-0.8337-0.22220.65410.2044-0.12891.18990.31851.3996-31.6114-83.49948.8373
201.3197-0.2692-0.162.648-0.33511.8750.06480.0809-0.3615-0.4581-0.1488-0.0795-0.1174-0.1780.03550.47580.2104-0.03740.40610.08370.3371-2.9968-78.5860.8655
210.31820.0548-0.03570.2958-0.06430.17180.1475-0.156-0.20590.203-0.19780.1320.40060.28250.04350.23610.33260.01130.4865-0.01680.2687-29.0712-42.7251-39.9565
220.0565-0.06910.04930.1739-0.01520.19380.05580.11960.0396-0.1977-0.1535-0.05350.11390.27320.0363-0.00330.4986-0.21190.7061-0.08810.3329-26.6937-39.4003-52.1328
230.1201-0.0388-0.10930.06660.08390.15980.07690.0049-0.10260.06720.05460.18020.1287-0.0057-0.03660.3530.1968-0.0450.3097-0.06790.3457-33.3661-45.6297-43.2713
240.6028-0.2375-0.18980.2177-0.07120.3021-0.05930.3723-0.27420.0168-0.230.27540.27170.20310.10940.24250.2097-0.02370.4118-0.04790.3049-25.8163-40.1627-43.9657
252.5814-0.80850.51091.0373-0.3471.2956-0.1891-0.85930.38980.4243-0.2965-0.4684-0.22191.14860.2414-0.04270.86770.08081.66360.07270.44093.016-43.3627-31.0954
261.97330.0911-0.80691.7496-0.43480.5002-0.1887-1.020.29920.5229-0.0837-0.1333-0.01970.65850.17810.55390.4489-0.1021.3250.21160.2429-5.4106-47.9417-29.0352
272.66451.0288-0.32982.7383-0.03230.05150.4001-1.32570.05891.2594-0.3498-0.57860.02780.56760.03620.20050.7107-0.19741.96870.15570.51861.818-44.0381-24.6034
280.8680.2668-0.56331.39750.43561.3567-0.03260.24160.4604-0.7218-0.10.0476-0.44430.30990.10550.52660.0222-0.00860.42520.04730.541-24.8716-18.9727-45.8151
290.3868-0.2081-0.82071.61840.2691.39690.01510.18260.64120.0617-0.0504-0.6021-0.47350.99490.0204-0.02750.05930.15051.25750.01490.6315-4.6614-32.4498-43.5852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:18 )A1 - 18
2X-RAY DIFFRACTION2( CHAIN A AND RESID 19:61 )A19 - 61
3X-RAY DIFFRACTION3( CHAIN A AND RESID 62:75 )A62 - 75
4X-RAY DIFFRACTION4( CHAIN A AND RESID 76:102 )A76 - 102
5X-RAY DIFFRACTION5( CHAIN A AND RESID 103:114 )A103 - 114
6X-RAY DIFFRACTION6( CHAIN A AND RESID 115:150 )A115 - 150
7X-RAY DIFFRACTION7( CHAIN A AND RESID 151:164 )A151 - 164
8X-RAY DIFFRACTION8( CHAIN A AND RESID 165:199 )A165 - 199
9X-RAY DIFFRACTION9( CHAIN A AND RESID 200:214 )A200 - 214
10X-RAY DIFFRACTION10( CHAIN B AND RESID 1:44 )B1 - 44
11X-RAY DIFFRACTION11( CHAIN B AND RESID 45:120 )B45 - 120
12X-RAY DIFFRACTION12( CHAIN B AND RESID 121:136 )B121 - 136
13X-RAY DIFFRACTION13( CHAIN B AND RESID 137:215 )B137 - 215
14X-RAY DIFFRACTION14( CHAIN C AND RESID 1:75 )C1 - 75
15X-RAY DIFFRACTION15( CHAIN C AND RESID 76:114 )C76 - 114
16X-RAY DIFFRACTION16( CHAIN C AND RESID 115:150 )C115 - 150
17X-RAY DIFFRACTION17( CHAIN C AND RESID 151:164 )C151 - 164
18X-RAY DIFFRACTION18( CHAIN C AND RESID 165:215 )C165 - 215
19X-RAY DIFFRACTION19( CHAIN D AND RESID 2:82 )D2 - 82
20X-RAY DIFFRACTION20( CHAIN D AND RESID 83:217 )D83 - 217
21X-RAY DIFFRACTION21( CHAIN E AND RESID 1:38 )E1 - 38
22X-RAY DIFFRACTION22( CHAIN E AND RESID 39:61 )E39 - 61
23X-RAY DIFFRACTION23( CHAIN E AND RESID 62:75 )E62 - 75
24X-RAY DIFFRACTION24( CHAIN E AND RESID 76:102 )E76 - 102
25X-RAY DIFFRACTION25( CHAIN E AND RESID 103:138 )E103 - 138
26X-RAY DIFFRACTION26( CHAIN E AND RESID 139:150 )E139 - 150
27X-RAY DIFFRACTION27( CHAIN E AND RESID 151:214 )E151 - 214
28X-RAY DIFFRACTION28( CHAIN F AND RESID 1:82 )F1 - 82
29X-RAY DIFFRACTION29( CHAIN F AND RESID 83:214 )F83 - 214

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