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- PDB-5trp: Crystal Structure of the Unliganded DH270 Cooperating Lineage Mem... -

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Basic information

Entry
Database: PDB / ID: 5trp
TitleCrystal Structure of the Unliganded DH270 Cooperating Lineage Member DH272
Components
  • DH272 Fab heavy chain
  • DH272 Fab light chain
KeywordsIMMUNE SYSTEM / FAB FRAGMENT / HIV-1 / ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.692 Å
AuthorsFera, D. / Harrison, S.C.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)1F32AI116355-01 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)UM-1- AI100645 United States
CitationJournal: Sci Transl Med / Year: 2017
Title: Staged induction of HIV-1 glycan-dependent broadly neutralizing antibodies.
Authors: Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O ...Authors: Mattia Bonsignori / Edward F Kreider / Daniela Fera / R Ryan Meyerhoff / Todd Bradley / Kevin Wiehe / S Munir Alam / Baptiste Aussedat / William E Walkowicz / Kwan-Ki Hwang / Kevin O Saunders / Ruijun Zhang / Morgan A Gladden / Anthony Monroe / Amit Kumar / Shi-Mao Xia / Melissa Cooper / Mark K Louder / Krisha McKee / Robert T Bailer / Brendan W Pier / Claudia A Jette / Garnett Kelsoe / Wilton B Williams / Lynn Morris / John Kappes / Kshitij Wagh / Gift Kamanga / Myron S Cohen / Peter T Hraber / David C Montefiori / Ashley Trama / Hua-Xin Liao / Thomas B Kepler / M Anthony Moody / Feng Gao / Samuel J Danishefsky / John R Mascola / George M Shaw / Beatrice H Hahn / Stephen C Harrison / Bette T Korber / Barton F Haynes /
Abstract: A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and ...A preventive HIV-1 vaccine should induce HIV-1-specific broadly neutralizing antibodies (bnAbs). However, bnAbs generally require high levels of somatic hypermutation (SHM) to acquire breadth, and current vaccine strategies have not been successful in inducing bnAbs. Because bnAbs directed against a glycosylated site adjacent to the third variable loop (V3) of the HIV-1 envelope protein require limited SHM, the V3-glycan epitope is an attractive vaccine target. By studying the cooperation among multiple V3-glycan B cell lineages and their coevolution with autologous virus throughout 5 years of infection, we identify key events in the ontogeny of a V3-glycan bnAb. Two autologous neutralizing antibody lineages selected for virus escape mutations and consequently allowed initiation and affinity maturation of a V3-glycan bnAb lineage. The nucleotide substitution required to initiate the bnAb lineage occurred at a low-probability site for activation-induced cytidine deaminase activity. Cooperation of B cell lineages and an improbable mutation critical for bnAb activity defined the necessary events leading to breadth in this V3-glycan bnAb lineage. These findings may, in part, explain why initiation of V3-glycan bnAbs is rare, and suggest an immunization strategy for inducing similar V3-glycan bnAbs.
History
DepositionOct 27, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Refinement description / Category: pdbx_audit_support / software
Item: _pdbx_audit_support.funding_organization / _software.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Oct 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
H: DH272 Fab heavy chain
L: DH272 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8904
Polymers49,5722
Non-polymers3172
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-38 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.862, 124.502, 146.159
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody DH272 Fab heavy chain


Mass: 25484.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / Production host: Homo sapiens (human)
#2: Antibody DH272 Fab light chain


Mass: 24087.764 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK 293T / Plasmid: pVRC-8400 / Cell line (production host): HEK 293T / 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: 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.: 1
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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / 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: 2.79 Å3/Da / Density % sol: 55.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.5 M AmSO4, 100 mM Na Acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97925 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 23, 2015
RadiationMonochromator: SINGLE CRYSTAL SI(220) SIDE BOUNCE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97925 Å / Relative weight: 1
ReflectionResolution: 2.68→47.389 Å / Num. obs: 15432 / % possible obs: 96 % / Redundancy: 1.7 % / Biso Wilson estimate: 39.52 Å2 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.113 / Rrim(I) all: 0.164 / Χ2: 1.032 / Net I/σ(I): 5.6 / Num. measured all: 47496
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.68-2.731.60.63814430.5380.6010.8790.9496.1
2.73-2.781.70.52614430.6520.4950.7240.89796.8
2.78-2.831.70.43414300.6670.4090.5980.98497.5
2.83-2.891.70.38214410.6870.3630.5280.9795.8
2.89-2.951.70.3314380.7240.3120.4551.00397.8
2.95-3.021.60.28414290.8090.2680.3911.02895.6
3.02-3.091.70.25614380.8570.2420.3531.09797.4
3.09-3.181.70.20214130.8830.1920.2791.02995.9
3.18-3.271.70.18614450.9050.1760.2561.13797.6
3.27-3.381.70.16714450.9170.1580.231.195.7
3.38-3.51.70.12914080.9460.1220.1781.05597
3.5-3.641.70.12214320.950.1160.1691.06996.4
3.64-3.81.70.11114040.9570.1050.1531.02795.2
3.8-41.70.09414460.9710.0890.131.09496.1
4-4.251.70.08214150.9760.0770.1131.08296.7
4.25-4.581.70.07514230.980.0710.1041.07495.1
4.58-5.041.70.07914070.9730.0750.1091.0595.1
5.04-5.771.70.06413990.9820.060.0881.01995.1
5.77-7.271.70.06513880.9840.0610.091.0193.8
7.27-501.80.05113760.9890.0480.070.96992.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.69 Å47.39 Å
Translation2.69 Å47.39 Å

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data reduction
HKL-2000data scaling
PHASER2.5.7phasing
PDB_EXTRACT3.2data extraction
Cootmodel building
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5F6I, 4LSS

5f6i

4lss


Resolution: 2.692→47.389 Å / FOM work R set: 0.7781 / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2561 832 5.39 %
Rwork0.2112 14600 -
obs0.2139 15432 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 121.83 Å2 / Biso mean: 51.43 Å2 / Biso min: 18.81 Å2
Refinement stepCycle: final / Resolution: 2.692→47.389 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3361 0 19 75 3455
Biso mean--47.32 40.1 -
Num. residues----439
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033497
X-RAY DIFFRACTIONf_angle_d0.8024757
X-RAY DIFFRACTIONf_chiral_restr0.053529
X-RAY DIFFRACTIONf_plane_restr0.005611
X-RAY DIFFRACTIONf_dihedral_angle_d13.6681245
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6917-2.86040.3711270.31932385251296
2.8604-3.08120.28451290.26242439256899
3.0812-3.39120.29851500.2282416256699
3.3912-3.88170.24131510.19612428257999
3.8817-4.88970.24281410.1622446258798
4.8897-47.39610.2081340.20812486262095
Refinement TLS params.Method: refined / Origin x: -11.6066 Å / Origin y: -25.2202 Å / Origin z: -48.3034 Å
111213212223313233
T0.1468 Å20.0264 Å2-0.0022 Å2-0.23 Å2-0.0169 Å2--0.2056 Å2
L0.5705 °2-0.2583 °20.0745 °2-1.365 °2-0.729 °2--1.9319 °2
S-0.0058 Å °-0.0937 Å °0.0357 Å °0.1286 Å °0.0979 Å °0.0401 Å °0.0486 Å °-0.0509 Å °-0.0727 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1
2X-RAY DIFFRACTION1allS1 - 70
3X-RAY DIFFRACTION1allS71 - 79
4X-RAY DIFFRACTION1allH1 - 222
5X-RAY DIFFRACTION1allL1 - 218

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