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- PDB-5f9o: Crystal structure of broadly neutralizing VH1-46 germline-derived... -

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Basic information

Entry
Database: PDB / ID: 5f9o
TitleCrystal structure of broadly neutralizing VH1-46 germline-derived CD4-binding site-directed antibody CH235.09 in complex with HIV-1 clade A/E 93TH057 gp120
Components
  • CH235.09 Light chain
  • CH235.9 Heavy chain
  • clade A/E 93TH057 HIV-1 gp120 core
KeywordsIMMUNE SYSTEM / antibody evolution HIV-1 broadly neutralizing CD4 binding site
Function / homology
Function and homology information


membrane fusion involved in viral entry into host cell / viral envelope / symbiont entry into host cell / virion attachment to host cell / virion membrane
Similarity search - Function
HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
clade A/E 93TH057 HIV-1 gp120 core
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.86 Å
AuthorsJoyce, M.G. / Mascola, J.R. / Kwong, P.D.
CitationJournal: Cell / Year: 2016
Title: Maturation Pathway from Germline to Broad HIV-1 Neutralizer of a CD4-Mimic Antibody.
Authors: Mattia Bonsignori / Tongqing Zhou / Zizhang Sheng / Lei Chen / Feng Gao / M Gordon Joyce / Gabriel Ozorowski / Gwo-Yu Chuang / Chaim A Schramm / Kevin Wiehe / S Munir Alam / Todd Bradley / ...Authors: Mattia Bonsignori / Tongqing Zhou / Zizhang Sheng / Lei Chen / Feng Gao / M Gordon Joyce / Gabriel Ozorowski / Gwo-Yu Chuang / Chaim A Schramm / Kevin Wiehe / S Munir Alam / Todd Bradley / Morgan A Gladden / Kwan-Ki Hwang / Sheelah Iyengar / Amit Kumar / Xiaozhi Lu / Kan Luo / Michael C Mangiapani / Robert J Parks / Hongshuo Song / Priyamvada Acharya / Robert T Bailer / Allen Cao / Aliaksandr Druz / Ivelin S Georgiev / Young D Kwon / Mark K Louder / Baoshan Zhang / Anqi Zheng / Brenna J Hill / Rui Kong / Cinque Soto / / James C Mullikin / Daniel C Douek / David C Montefiori / Michael A Moody / George M Shaw / Beatrice H Hahn / Garnett Kelsoe / Peter T Hraber / Bette T Korber / Scott D Boyd / Andrew Z Fire / Thomas B Kepler / Lawrence Shapiro / Andrew B Ward / John R Mascola / Hua-Xin Liao / Peter D Kwong / Barton F Haynes /
Abstract: Antibodies with ontogenies from VH1-2 or VH1-46-germline genes dominate the broadly neutralizing response against the CD4-binding site (CD4bs) on HIV-1. Here, we define with longitudinal sampling ...Antibodies with ontogenies from VH1-2 or VH1-46-germline genes dominate the broadly neutralizing response against the CD4-binding site (CD4bs) on HIV-1. Here, we define with longitudinal sampling from time-of-infection the development of a VH1-46-derived antibody lineage that matured to neutralize 90% of HIV-1 isolates. Structures of lineage antibodies CH235 (week 41 from time-of-infection, 18% breadth), CH235.9 (week 152, 77%), and CH235.12 (week 323, 90%) demonstrated the maturing epitope to focus on the conformationally invariant portion of the CD4bs. Similarities between CH235 lineage and five unrelated CD4bs lineages in epitope focusing, length-of-time to develop breadth, and extraordinary level of somatic hypermutation suggested commonalities in maturation among all CD4bs antibodies. Fortunately, the required CH235-lineage hypermutation appeared substantially guided by the intrinsic mutability of the VH1-46 gene, which closely resembled VH1-2. We integrated our CH235-lineage findings with a second broadly neutralizing lineage and HIV-1 co-evolution to suggest a vaccination strategy for inducing both lineages.
History
DepositionDec 10, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Mar 23, 2016Group: Database references
Revision 1.2Apr 20, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _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
G: clade A/E 93TH057 HIV-1 gp120 core
H: CH235.9 Heavy chain
L: CH235.09 Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,49418
Polymers87,8333
Non-polymers4,66115
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9540 Å2
ΔGint34 kcal/mol
Surface area35610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.530, 67.803, 225.617
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 2 molecules HL

#2: Antibody CH235.9 Heavy chain


Mass: 25218.555 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody CH235.09 Light chain


Mass: 23532.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Protein / Sugars , 2 types, 13 molecules G

#1: Protein clade A/E 93TH057 HIV-1 gp120 core


Mass: 39082.320 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: HIV-1 Env / Production host: Homo sapiens (human) / References: UniProt: A0A0M3KKW9
#4: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 463 molecules

#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.77 Å3/Da / Density % sol: 55.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 9% (w/v) PEG8000, 19% (w/v) of PEG400, 0.1 M HEPES pH 7.5
PH range: 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Aug 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8599→50 Å / Num. obs: 73935 / % possible obs: 89.7 % / Redundancy: 3.4 % / Net I/σ(I): 7.06

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementResolution: 1.86→35.815 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.48 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2205 3556 4.81 %
Rwork0.2039 --
obs0.2048 73935 89.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→35.815 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5967 0 221 460 6648
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0166347
X-RAY DIFFRACTIONf_angle_d1.2748602
X-RAY DIFFRACTIONf_dihedral_angle_d17.6222300
X-RAY DIFFRACTIONf_chiral_restr0.039985
X-RAY DIFFRACTIONf_plane_restr0.0041086
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8599-1.88540.3539490.32491019X-RAY DIFFRACTION33
1.8854-1.91230.3318790.3331484X-RAY DIFFRACTION48
1.9123-1.94090.36581060.3091891X-RAY DIFFRACTION60
1.9409-1.97120.30521060.29622204X-RAY DIFFRACTION71
1.9712-2.00350.3211190.27752435X-RAY DIFFRACTION78
2.0035-2.0380.31991340.26222602X-RAY DIFFRACTION84
2.038-2.07510.31580.24932714X-RAY DIFFRACTION87
2.0751-2.1150.26751450.26222964X-RAY DIFFRACTION94
2.115-2.15820.28431590.25622930X-RAY DIFFRACTION95
2.1582-2.20510.28891290.24743032X-RAY DIFFRACTION96
2.2051-2.25640.2711450.22973068X-RAY DIFFRACTION97
2.2564-2.31280.25221540.23273047X-RAY DIFFRACTION98
2.3128-2.37530.28271750.23323088X-RAY DIFFRACTION99
2.3753-2.44520.24351540.23383132X-RAY DIFFRACTION99
2.4452-2.52410.25841600.24313110X-RAY DIFFRACTION100
2.5241-2.61430.26921610.23823105X-RAY DIFFRACTION99
2.6143-2.71890.24161530.22223152X-RAY DIFFRACTION99
2.7189-2.84260.24831500.22193125X-RAY DIFFRACTION99
2.8426-2.99240.23091530.21973163X-RAY DIFFRACTION100
2.9924-3.17980.26261580.21583158X-RAY DIFFRACTION99
3.1798-3.42510.20041540.19553162X-RAY DIFFRACTION99
3.4251-3.76950.19291610.18773165X-RAY DIFFRACTION99
3.7695-4.31410.16711530.16363174X-RAY DIFFRACTION99
4.3141-5.43230.1561840.15433184X-RAY DIFFRACTION98
5.4323-35.82130.22541570.19853271X-RAY DIFFRACTION95
Refinement TLS params.Method: refined / Origin x: 3.2729 Å / Origin y: -23.8821 Å / Origin z: -27.8733 Å
111213212223313233
T0.2597 Å20.0165 Å20.003 Å2-0.2231 Å2-0.0194 Å2--0.2934 Å2
L0.3662 °20.1012 °2-0.2126 °2-0.3468 °2-0.2804 °2--0.8005 °2
S-0.0286 Å °0.0324 Å °-0.0812 Å °-0.0125 Å °-0.0562 Å °-0.0354 Å °0.0695 Å °0.0954 Å °0.0918 Å °
Refinement TLS groupSelection details: all

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