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Basic information

Entry
Database: PDB / ID: 7ti6
TitleCrystal structure of the wild-type least mutated common ancestor (LMCA) of the HIV-targeting PCT64 antibody lineage
Components
  • PCT64_LMCA Fab heavy chain
  • PCT64_LMCA light chain (wild type)
KeywordsIMMUNE SYSTEM / Antibody / Broadly Neutralizing / HIV-1 / V2 Apex
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.64 Å
AuthorsOmorodion, O. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI144462 United States
Bill & Melinda Gates FoundationOPP119635 United States
CitationJournal: Immunity / Year: 2022
Title: Human immunoglobulin repertoire analysis guides design of vaccine priming immunogens targeting HIV V2-apex broadly neutralizing antibody precursors.
Authors: Jordan R Willis / Zachary T Berndsen / Krystal M Ma / Jon M Steichen / Torben Schiffner / Elise Landais / Alessia Liguori / Oleksandr Kalyuzhniy / Joel D Allen / Sabyasachi Baboo / ...Authors: Jordan R Willis / Zachary T Berndsen / Krystal M Ma / Jon M Steichen / Torben Schiffner / Elise Landais / Alessia Liguori / Oleksandr Kalyuzhniy / Joel D Allen / Sabyasachi Baboo / Oluwarotimi Omorodion / Jolene K Diedrich / Xiaozhen Hu / Erik Georgeson / Nicole Phelps / Saman Eskandarzadeh / Bettina Groschel / Michael Kubitz / Yumiko Adachi / Tina-Marie Mullin / Nushin B Alavi / Samantha Falcone / Sunny Himansu / Andrea Carfi / Ian A Wilson / John R Yates / James C Paulson / Max Crispin / Andrew B Ward / William R Schief /
Abstract: Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain ...Broadly neutralizing antibodies (bnAbs) to the HIV envelope (Env) V2-apex region are important leads for HIV vaccine design. Most V2-apex bnAbs engage Env with an uncommonly long heavy-chain complementarity-determining region 3 (HCDR3), suggesting that the rarity of bnAb precursors poses a challenge for vaccine priming. We created precursor sequence definitions for V2-apex HCDR3-dependent bnAbs and searched for related precursors in human antibody heavy-chain ultradeep sequencing data from 14 HIV-unexposed donors. We found potential precursors in a majority of donors for only two long-HCDR3 V2-apex bnAbs, PCT64 and PG9, identifying these bnAbs as priority vaccine targets. We then engineered ApexGT Env trimers that bound inferred germlines for PCT64 and PG9 and had higher affinities for bnAbs, determined cryo-EM structures of ApexGT trimers complexed with inferred-germline and bnAb forms of PCT64 and PG9, and developed an mRNA-encoded cell-surface ApexGT trimer. These methods and immunogens have promise to assist HIV vaccine development.
History
DepositionJan 12, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: 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.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: PCT64_LMCA Fab heavy chain
L: PCT64_LMCA light chain (wild type)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3473
Polymers49,1092
Non-polymers2381
Water37821
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: mass spectrometry, gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-19 kcal/mol
Surface area20290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.083, 64.317, 76.324
Angle α, β, γ (deg.)90.000, 98.182, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Antibody PCT64_LMCA Fab heavy chain


Mass: 25605.490 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 PCT64_LMCA light chain (wild type)


Mass: 23503.041 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: N-terminal residues "VH" originate from the signal peptide
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Sequence detailsThis Fab was isolated as part of an antibody lineage from an HIV-infected human donor. Within said ...This Fab was isolated as part of an antibody lineage from an HIV-infected human donor. Within said lineage, its sequence is closest to the antibody germline; it is the least mutated member of the family.

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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: 2.77 Å3/Da / Density % sol: 55.67 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / Details: 0.1 M HEPES (pH 6.5), 12% (w/v) PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03319 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03319 Å / Relative weight: 1
ReflectionResolution: 2.64→50 Å / Num. obs: 15988 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 47.19 Å2 / CC1/2: 0.83 / Rpim(I) all: 0.11 / Rsym value: 0.25 / Net I/σ(I): 8.7
Reflection shellResolution: 2.64→2.69 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 1.4 / Num. unique obs: 811 / CC1/2: 0.34 / Rpim(I) all: 0.87 / Rsym value: 1.91 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-20002.3.10data reduction
SCALEPACKdata scaling
PHASER2.8.2phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CA7

6ca7


Resolution: 2.64→48.97 Å / SU ML: 0.4915 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.9551
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.253 769 4.81 %
Rwork0.2287 15205 -
obs0.2299 15974 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 61.8 Å2
Refinement stepCycle: LAST / Resolution: 2.64→48.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3392 0 15 21 3428
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00213487
X-RAY DIFFRACTIONf_angle_d0.58914741
X-RAY DIFFRACTIONf_chiral_restr0.0421527
X-RAY DIFFRACTIONf_plane_restr0.0046604
X-RAY DIFFRACTIONf_dihedral_angle_d17.64131246
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.64-2.840.41341560.34353009X-RAY DIFFRACTION99.62
2.84-3.130.35731600.32453008X-RAY DIFFRACTION99.94
3.13-3.580.31741290.26063060X-RAY DIFFRACTION99.97
3.58-4.510.21681530.20033037X-RAY DIFFRACTION99.87
4.51-48.970.18511710.17313091X-RAY DIFFRACTION99.97
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)
13.33505687668-0.533776522736-1.156282338521.92091377168-1.923345207068.19079036293-0.036493932303-0.3587460739680.10564030659-0.2128662932370.181066437041-0.3806191718410.376569715543-0.0156127043422-0.203259585790.324604624458-0.04339972894060.03680379696730.2300355314920.0195933997420.57484004523351.241-3.50928.074
29.09829169097-1.732749908586.034423395764.409676433370.4802863927648.025095730970.00867683374393-2.673095386090.05150948919331.352147889440.768517273821-0.410827624432-1.00209901994-1.64427186804-0.3524949799090.656710919090.03851364712740.03129612438230.879158691443-0.07222912687670.84119849376147.4321.1642.104
34.27695124855-1.54671920448-0.9830584482696.73195600916-0.5526104691984.35750882885-0.0119135402965-0.4195660391510.228864113908-0.4656237722880.02861037551520.352618438-0.436229220918-0.3226503355860.02225610561510.442536161817-0.0188661446209-0.02324009340540.287814949784-0.006667565096680.4247564884230.14519.3047.633
43.348992439580.179680843589-0.3945682900071.7881062269-1.043152433572.333361372880.206621670151-0.4983187908990.2712902264260.6184543873411.09943491014-0.3751421864521.58518196824-2.88742447895-0.4658774143870.249120661719-0.4662382924410.176292655381.995254098580.7372902726070.29146069296930.633-8.00736.215
52.52225269452-1.351025199153.121809153752.965427523530.2426666215850.700546562795-0.245502166643-1.44989322993-0.3251604880920.1241087713230.3428541287850.08669756579210.245142218364-1.02982427817-0.03231194647180.188284093292-0.03598013353260.1506840173181.147153379950.2972296145210.49541544109926.2333.23121.752
66.332710385060.715467467697-1.943609199961.845409504480.07336301525146.82123113054-0.0273546965839-0.911799195856-0.24977863785-0.1413456140450.153161052860.08855543203640.0964709409008-0.0118457997084-0.1143279378410.3408026996860.042463695072-0.001608635380560.3288297857890.1281465403960.52648076437418.9526.1215.118
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN H AND RESID 1:100 )H1 - 100
2X-RAY DIFFRACTION2( CHAIN H AND RESID 101:109 )H101 - 109
3X-RAY DIFFRACTION3( CHAIN H AND RESID 110:217 )H110 - 217
4X-RAY DIFFRACTION4( CHAIN L AND RESID -1:75 )L-1 - 75
5X-RAY DIFFRACTION5( CHAIN L AND RESID 76:128 )L76 - 128
6X-RAY DIFFRACTION6( CHAIN L AND RESID 129:213 )L129 - 213

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