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- PDB-8te7: Structure of TRNM-f.01 -

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Basic information

Entry
Database: PDB / ID: 8te7
TitleStructure of TRNM-f.01
Components
  • TRNM-f.01 Fab Heavy Chain
  • TRNM-f.01 Fab Light Chain
KeywordsIMMUNE SYSTEM / HIV-1 / CD4 Binding Site / Antibody / Fab
Biological speciesMacaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.18 Å
AuthorsBender, M.F. / Olia, A.S. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Cell / Year: 2024
Title: Potent and broad HIV-1 neutralization in fusion peptide-primed SHIV-infected macaques.
Authors: Hua Wang / Cheng Cheng / James L Dal Santo / Chen-Hsiang Shen / Tatsiana Bylund / Amy R Henry / Colin A Howe / Juyun Hwang / Nicholas C Morano / Daniel J Morris / Sergei Pletnev / Ryan S ...Authors: Hua Wang / Cheng Cheng / James L Dal Santo / Chen-Hsiang Shen / Tatsiana Bylund / Amy R Henry / Colin A Howe / Juyun Hwang / Nicholas C Morano / Daniel J Morris / Sergei Pletnev / Ryan S Roark / Tongqing Zhou / Bryan T Hansen / Forrest H Hoyt / Timothy S Johnston / Shuyi Wang / Baoshan Zhang / David R Ambrozak / Jordan E Becker / Michael F Bender / Anita Changela / Ridhi Chaudhary / Martin Corcoran / Angela R Corrigan / Kathryn E Foulds / Yicheng Guo / Myungjin Lee / Yingying Li / Bob C Lin / Tracy Liu / Mark K Louder / Marco Mandolesi / Rosemarie D Mason / Krisha McKee / Vinod Nair / Sijy O'Dell / Adam S Olia / Li Ou / Amarendra Pegu / Nagarajan Raju / Reda Rawi / Jesmine Roberts-Torres / Edward K Sarfo / Mallika Sastry / Andrew J Schaub / Stephen D Schmidt / Chaim A Schramm / Cindi L Schwartz / Sarah C Smith / Tyler Stephens / Jonathan Stuckey / I-Ting Teng / John-Paul Todd / Yaroslav Tsybovsky / David J Van Wazer / Shuishu Wang / Nicole A Doria-Rose / Elizabeth R Fischer / Ivelin S Georgiev / Gunilla B Karlsson Hedestam / Zizhang Sheng / Ruth A Woodward / Daniel C Douek / Richard A Koup / Theodore C Pierson / Lawrence Shapiro / George M Shaw / John R Mascola / Peter D Kwong /
Abstract: An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the ...An antibody-based HIV-1 vaccine will require the induction of potent cross-reactive HIV-1-neutralizing responses. To demonstrate feasibility toward this goal, we combined vaccination targeting the fusion-peptide site of vulnerability with infection by simian-human immunodeficiency virus (SHIV). In four macaques with vaccine-induced neutralizing responses, SHIV infection boosted plasma neutralization to 45%-77% breadth (geometric mean 50% inhibitory dilution [ID] ∼100) on a 208-strain panel. Molecular dissection of these responses by antibody isolation and cryo-electron microscopy (cryo-EM) structure determination revealed 15 of 16 antibody lineages with cross-clade neutralization to be directed toward the fusion-peptide site of vulnerability. In each macaque, isolated antibodies from memory B cells recapitulated the plasma-neutralizing response, with fusion-peptide-binding antibodies reaching breadths of 40%-60% (50% inhibitory concentration [IC] < 50 μg/mL) and total lineage-concentrations estimates of 50-200 μg/mL. Longitudinal mapping indicated that these responses arose prior to SHIV infection. Collectively, these results provide in vivo molecular examples for one to a few B cell lineages affording potent, broadly neutralizing plasma responses.
History
DepositionJul 5, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 10, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 1.2Nov 13, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 25, 2024Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.4Jan 15, 2025Group: Database references / Category: citation / Item: _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: TRNM-f.01 Fab Heavy Chain
C: TRNM-f.01 Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,6672
Polymers48,6672
Non-polymers00
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-28 kcal/mol
Surface area20120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)136.895, 136.895, 94.903
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody TRNM-f.01 Fab Heavy Chain


Mass: 25525.371 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#2: Antibody TRNM-f.01 Fab Light Chain


Mass: 23141.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 5.27 Å3/Da / Density % sol: 76.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M LiSO4 1.3 M NaH2PO4 0.8 M KH2PO4 0.1 M CAPS pH 10.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 1, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.18→50 Å / Num. obs: 17587 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.988 / CC star: 0.997 / Rmerge(I) obs: 0.124 / Rrim(I) all: 0.134 / Net I/σ(I): 19.45
Reflection shellResolution: 3.18→3.26 Å / Num. unique obs: 844 / CC1/2: 0.824 / CC star: 0.95

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-2000data reduction
SERGUIdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.18→44.81 Å / SU ML: 0.54 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2625 1720 9.91 %
Rwork0.2325 --
obs0.2354 17358 98.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.18→44.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3372 0 0 82 3454
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053448
X-RAY DIFFRACTIONf_angle_d1.0054699
X-RAY DIFFRACTIONf_dihedral_angle_d7.902480
X-RAY DIFFRACTIONf_chiral_restr0.053540
X-RAY DIFFRACTIONf_plane_restr0.01600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.18-3.270.44161440.40381277X-RAY DIFFRACTION98
3.27-3.380.41861380.3621256X-RAY DIFFRACTION98
3.38-3.50.411440.30141289X-RAY DIFFRACTION98
3.5-3.640.31861450.28811276X-RAY DIFFRACTION99
3.64-3.810.31191470.28181312X-RAY DIFFRACTION99
3.81-4.010.33061390.2561283X-RAY DIFFRACTION99
4.01-4.260.26631460.21671315X-RAY DIFFRACTION99
4.26-4.590.20621400.1911297X-RAY DIFFRACTION100
4.59-5.050.20811430.18681313X-RAY DIFFRACTION99
5.05-5.770.25261440.19651306X-RAY DIFFRACTION100
5.78-7.270.22931470.23411343X-RAY DIFFRACTION99
7.28-44.810.2041430.20791371X-RAY DIFFRACTION97

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