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- PDB-6ca6: Crystal structure of PCT64_35S, a broadly neutralizing anti-HIV a... -

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Basic information

Entry
Database: PDB / ID: 6ca6
TitleCrystal structure of PCT64_35S, a broadly neutralizing anti-HIV antibody.
Components
  • PCT64_35S heavy chain
  • PCT64_35S light chain
KeywordsIMMUNE SYSTEM / Antibody / neutralizing
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.43 Å
AuthorsMurrell, S. / Wilson, I.A.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM1 AI100663 United States
International AIDS Vaccine InitiativeOPP1084519 United States
CitationJournal: Cell Rep / Year: 2018
Title: Co-evolution of HIV Envelope and Apex-Targeting Neutralizing Antibody Lineage Provides Benchmarks for Vaccine Design.
Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais ...Authors: Kimmo Rantalainen / Zachary T Berndsen / Sasha Murrell / Liwei Cao / Oluwarotimi Omorodion / Jonathan L Torres / Mengyu Wu / Jeffrey Umotoy / Jeffrey Copps / Pascal Poignard / Elise Landais / James C Paulson / Ian A Wilson / Andrew B Ward /
Abstract: Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at ...Broadly neutralizing antibodies (bnAbs) targeting the HIV envelope glycoprotein (Env) typically take years to develop. Longitudinal analyses of both neutralizing antibody lineages and viruses at serial time points during infection provide a basis for understanding the co-evolutionary contest between HIV and the humoral immune system. Here, we describe the structural characterization of an apex-targeting antibody lineage and autologous clade A viral Env from a donor in the Protocol C cohort. Comparison of Ab-Env complexes at early and late time points reveals that, within the antibody lineage, the CDRH3 loop rigidifies, the bnAb angle of approach steepens, and surface charges are mutated to accommodate glycan changes. Additionally, we observed differences in site-specific glycosylation between soluble and full-length Env constructs, which may be important for tuning optimal immunogenicity in soluble Env trimers. These studies therefore provide important guideposts for design of immunogens that prime and mature nAb responses to the Env V2-apex.
History
DepositionJan 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Mar 16, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: PCT64_35S light chain
H: PCT64_35S heavy chain
A: PCT64_35S light chain
B: PCT64_35S heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,7189
Polymers98,2434
Non-polymers4745
Water3,243180
1
L: PCT64_35S light chain
H: PCT64_35S heavy chain


Theoretical massNumber of molelcules
Total (without water)49,1222
Polymers49,1222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3020 Å2
ΔGint-20 kcal/mol
Surface area21030 Å2
MethodPISA
2
A: PCT64_35S light chain
B: PCT64_35S heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5967
Polymers49,1222
Non-polymers4745
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-19 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.776, 98.132, 100.563
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody PCT64_35S light chain


Mass: 23525.029 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody PCT64_35S heavy chain


Mass: 25596.633 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 0.17M sodium acetate, 0.085M Tris pH 8.5, 15% glycerol and 25.5% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0332 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.43→50 Å / Num. obs: 36695 / % possible obs: 99.7 % / Redundancy: 11.4 % / Net I/σ(I): 18.3
Reflection shellResolution: 2.43→2.47 Å / Num. unique all: 1716 / Rpim(I) all: 0.26

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5FEH

5feh


Resolution: 2.43→49.066 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.245 1872 5.12 %
Rwork0.2014 --
obs0.2037 36587 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.43→49.066 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6728 0 31 180 6939
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066942
X-RAY DIFFRACTIONf_angle_d0.8669442
X-RAY DIFFRACTIONf_dihedral_angle_d18.292508
X-RAY DIFFRACTIONf_chiral_restr0.0551046
X-RAY DIFFRACTIONf_plane_restr0.0061209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.43-2.49570.29941240.26332557X-RAY DIFFRACTION96
2.4957-2.56910.34591670.25422589X-RAY DIFFRACTION99
2.5691-2.65210.26241360.24772678X-RAY DIFFRACTION100
2.6521-2.74680.29011190.2412633X-RAY DIFFRACTION100
2.7468-2.85680.31771650.23892647X-RAY DIFFRACTION100
2.8568-2.98680.28651940.23682613X-RAY DIFFRACTION100
2.9868-3.14430.28321020.22852694X-RAY DIFFRACTION100
3.1443-3.34120.23641110.22272709X-RAY DIFFRACTION100
3.3412-3.59910.27341450.20312667X-RAY DIFFRACTION100
3.5991-3.96120.23691730.19032654X-RAY DIFFRACTION100
3.9612-4.5340.22351180.15692733X-RAY DIFFRACTION100
4.534-5.7110.19341530.15772733X-RAY DIFFRACTION100
5.711-49.0760.18991650.18912808X-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)
10.82220.3401-2.03861.67460.63538.15480.00160.2968-0.043-0.0366-0.11670.6948-0.1676-0.60690.10990.20180.0309-0.07820.3249-0.06710.5171113.8143121.0316110.9842
23.3735-3.3377-0.847.00142.20274.27340.25780.12320.0376-0.5635-0.0875-0.0075-0.17860.1989-0.14620.2958-0.0381-0.05650.20770.01340.2304125.0471125.0763115.1473
33.7094-1.0022-2.42264.66411.9976.81260.04810.23620.2422-0.18860.00630.2624-0.7102-0.3758-0.0720.23560.0408-0.05090.1865-0.03910.2809120.4082128.9914110.5244
40.1785-0.4845-1.67461.49972.59478.52960.21440.02990.0302-0.08320.0287-0.0505-0.1381-0.1599-0.22250.20450.03520.00450.27910.02320.296120.2468117.5111108.1409
51.17631.90950.17983.13010.33793.65280.11110.0519-0.15420.2922-0.0037-0.12960.54340.2709-0.09930.2850.0665-0.05240.24490.01290.2012128.40193.264196.3688
62.1985-1.03290.216.6582-0.45982.63840.1260.0304-0.05970.1735-0.0925-0.1910.36630.142-0.02530.2822-0.012-0.06830.24720.00680.2069130.370798.142897.9755
74.0061-0.22671.87167.0251-1.64285.07520.13640.1506-0.2746-0.40490.04480.42760.67830.2844-0.11970.38390.0153-0.08160.2018-0.03010.3105124.479490.032689.2905
82.4474-1.00530.52453.09572.53182.7694-0.2988-0.12840.05380.2910.3577-0.88610.11980.2736-0.09670.10250.017-0.01720.29820.00440.1904139.398112.59125.3964
90.61270.3549-0.50644.5527-1.07081.94690.0634-0.06820.08370.5094-0.1377-0.0966-0.00080.13890.05170.2238-0.00790.00350.20570.00170.2519131.0309116.5789130.8145
100.5296-0.263-0.38742.0540.40261.3736-0.00940.11840.12870.40110.1077-0.2107-0.2487-0.0144-0.08860.2363-0.0151-0.00720.30160.00760.2344133.0769138.6505121.3812
110.5834-0.3581.30451.48330.17325.3615-0.03410.0646-0.02320.17120.2173-0.12620.23150.3049-0.17540.17190.0545-0.00140.29620.03170.3021139.8552102.4885118.7342
121.7823-0.67391.66062.2919-1.24656.6610.02170.5030.0344-0.251-0.2319-0.1448-0.05361.20490.17470.22420.0079-0.01050.41130.03280.2429140.640299.55897.9919
131.6053-0.76130.55081.468-1.66835.17330.15131.12830.3248-0.2043-0.3061-0.74220.01362.08350.25350.32850.0982-0.01830.9250.11750.4873149.114598.1377100.4158
143.2092.22951.37326.2392-0.04581.8339-0.02080.2059-0.2670.1460.1424-0.74730.36370.5228-0.13080.28010.11090.00940.4048-0.06570.3229149.1406133.731299.6837
152.75362.35061.03144.66641.79953.37070.2908-0.17350.0136-0.2278-0.0955-0.49150.38270.3457-0.16380.26050.144-0.00790.3607-0.04530.3231144.0889131.12894.2963
160.96980.64360.38141.24440.15223.16710.0360.71010.0231-0.7775-0.3717-0.30590.65480.88010.31360.73980.28890.12440.66410.09170.3886131.1306125.913567.1042
171.8096-0.11441.48141.28610.68387.4008-0.0449-0.04530.16490.04170.1150.3717-0.5608-0.4536-0.07990.24870.03020.0780.28650.04070.4498131.8326154.026892.3954
181.68091.01851.37862.42130.73315.90270.04910.13380.35420.03870.1673-0.0173-0.37340.4867-0.16490.2192-0.02340.10250.25340.01930.309142.3391153.997699.0328
190.17250.4269-0.19221.5504-0.68865.89250.16870.01950.12650.12380.0207-0.1115-0.53090.6907-0.19980.1816-0.0140.06830.2834-0.02520.3339140.6594150.9401104.4661
204.26030.53113.85631.45851.68634.41720.11230.10130.0223-0.31910.38860.2816-0.253-0.5405-0.45290.21710.0213-0.01720.30890.12490.3862128.5935150.280481.3193
212.4631-0.28860.38724.2254-0.88942.29020.06450.16-0.1923-0.6207-0.2205-0.26810.43040.21470.1430.39060.0807-0.00770.27860.07120.2426121.6051132.780275.3047
225.64452.29860.9018.06072.6535.94270.20090.2234-0.1768-0.302-0.34020.94740.553-0.24990.1320.34480.0744-0.0920.2660.03090.2982112.497134.105274.8033
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'L' and (resid 1 through 29 )
2X-RAY DIFFRACTION2chain 'L' and (resid 30 through 48 )
3X-RAY DIFFRACTION3chain 'L' and (resid 49 through 90 )
4X-RAY DIFFRACTION4chain 'L' and (resid 91 through 113 )
5X-RAY DIFFRACTION5chain 'L' and (resid 114 through 163 )
6X-RAY DIFFRACTION6chain 'L' and (resid 164 through 187 )
7X-RAY DIFFRACTION7chain 'L' and (resid 188 through 213 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 17 )
9X-RAY DIFFRACTION9chain 'H' and (resid 18 through 87 )
10X-RAY DIFFRACTION10chain 'H' and (resid 88 through 103 )
11X-RAY DIFFRACTION11chain 'H' and (resid 104 through 119 )
12X-RAY DIFFRACTION12chain 'H' and (resid 120 through 193 )
13X-RAY DIFFRACTION13chain 'H' and (resid 194 through 213 )
14X-RAY DIFFRACTION14chain 'A' and (resid 2 through 75 )
15X-RAY DIFFRACTION15chain 'A' and (resid 76 through 113 )
16X-RAY DIFFRACTION16chain 'A' and (resid 114 through 212 )
17X-RAY DIFFRACTION17chain 'B' and (resid 1 through 17 )
18X-RAY DIFFRACTION18chain 'B' and (resid 18 through 59 )
19X-RAY DIFFRACTION19chain 'B' and (resid 60 through 103 )
20X-RAY DIFFRACTION20chain 'B' and (resid 104 through 119 )
21X-RAY DIFFRACTION21chain 'B' and (resid 120 through 188 )
22X-RAY DIFFRACTION22chain 'B' and (resid 189 through 213 )

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