[English] 日本語
Yorodumi
- PDB-9b44: Crystal structure of mAb 8-24 Fab, a VRC01-like HIV-1 antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9b44
TitleCrystal structure of mAb 8-24 Fab, a VRC01-like HIV-1 antibody
Components
  • MLK8-24 Fab Heavy Chain
  • MLK8-24 Fab Light Chain
KeywordsIMMUNE SYSTEM / HIV Antibody
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.01 Å
AuthorsKher, G. / Hurlburt, N. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI138212-05 United States
CitationJournal: J Virol / Year: 2024
Title: Short CDRL1 in intermediate VRC01-like mAbs is not sufficient to overcome key glycan barriers on HIV-1 Env.
Authors: Parul Agrawal / Maria L Knudsen / Anna MacCamy / Nicholas K Hurlburt / Arineh Khechaduri / Kelsey R Salladay / Gargi M Kher / Latha Kallur Siddaramaiah / Andrew B Stuart / Ilja Bontjer / ...Authors: Parul Agrawal / Maria L Knudsen / Anna MacCamy / Nicholas K Hurlburt / Arineh Khechaduri / Kelsey R Salladay / Gargi M Kher / Latha Kallur Siddaramaiah / Andrew B Stuart / Ilja Bontjer / Xiaoying Shen / David Montefiori / Harry B Gristick / Pamela J Bjorkman / Rogier W Sanders / Marie Pancera / Leonidas Stamatatos /
Abstract: VRC01-class broadly neutralizing antibodies (bnAbs) have been isolated from people with HIV-1, but they have not yet been elicited by vaccination. They are extensively somatically mutated and ...VRC01-class broadly neutralizing antibodies (bnAbs) have been isolated from people with HIV-1, but they have not yet been elicited by vaccination. They are extensively somatically mutated and sometimes accumulate CDRL1 deletions. Such indels may allow VRC01-class antibodies to accommodate the glycans expressed on a conserved N276 N-linked glycosylation site in loop D of the gp120 subunit. These glycans constitute a major obstacle in the development of VRC01-class antibodies, as unmutated antibody forms are unable to accommodate them. Although immunizations of knock-in mice expressing human VRC01-class B-cell receptors (BCRs) with specifically designed Env-derived immunogens lead to the accumulation of somatic mutations in VRC01-class BCRs, CDRL1 deletions are rarely observed, and the elicited antibodies display narrow neutralizing activities. The lack of broad neutralizing potential could be due to the absence of deletions, the lack of appropriate somatic mutations, or both. To address this point, we modified our previously determined prime-boost immunization with a germline-targeting immunogen nanoparticle (426c.Mod.Core), followed by a heterologous core nanoparticle (HxB2.WT.Core), by adding a final boost with a cocktail of various stabilized soluble Env trimers. We isolated VRC01-like antibodies with extensive somatic mutations and, in one case, a seven-amino acid CDRL1 deletion. We generated chimeric antibodies that combine the vaccine-elicited somatic mutations with CDRL1 deletions present in human mature VRC01 bnAbs. We observed that CDRL1 indels did not improve the neutralizing antibody activities. Our study indicates that CDRL1 length by itself is not sufficient for the broadly neutralizing phenotype of this class of antibodies.
IMPORTANCE: HIV-1 broadly neutralizing antibodies will be a key component of an effective HIV-1 vaccine, as they prevent viral acquisition. Over the past decade, numerous broadly neutralizing ...IMPORTANCE: HIV-1 broadly neutralizing antibodies will be a key component of an effective HIV-1 vaccine, as they prevent viral acquisition. Over the past decade, numerous broadly neutralizing antibodies (bnAbs) have been isolated from people with HIV. Despite an in-depth knowledge of their structures, epitopes, ontogenies, and, in a few rare cases, their maturation pathways during infection, bnAbs have, so far, not been elicited by vaccination. This necessitates the identification of key obstacles that prevent their elicitation by immunization and overcoming them. Here we examined whether CDRL1 shortening is a prerequisite for the broadly neutralizing potential of VRC01-class bnAbs, which bind within the CD4 receptor binding site of Env. Our findings indicate that CDRL1 shortening by itself is important but not sufficient for the acquisition of neutralization breadth, and suggest that particular combinations of amino acid mutations, not elicited so far by vaccination, are most likely required for the development of such a feature.
History
DepositionMar 20, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 4, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 26, 2025Group: 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.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MLK8-24 Fab Heavy Chain
B: MLK8-24 Fab Light Chain
H: MLK8-24 Fab Heavy Chain
L: MLK8-24 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,19414
Polymers98,5744
Non-polymers62110
Water2,576143
1
A: MLK8-24 Fab Heavy Chain
B: MLK8-24 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6598
Polymers49,2872
Non-polymers3726
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-12 kcal/mol
Surface area19580 Å2
MethodPISA
2
H: MLK8-24 Fab Heavy Chain
L: MLK8-24 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5356
Polymers49,2872
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4170 Å2
ΔGint-6 kcal/mol
Surface area19630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.874, 77.699, 266.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Antibody MLK8-24 Fab Heavy Chain


Mass: 25543.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody MLK8-24 Fab Light Chain


Mass: 23743.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.196 Å3/Da / Density % sol: 43.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG3350, 0.4M KSCN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 3, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.01→44.36 Å / Num. obs: 58632 / % possible obs: 99.1 % / Redundancy: 5.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.049 / Rrim(I) all: 0.121 / Χ2: 1 / Net I/σ(I): 10 / Num. measured all: 340358
Reflection shellResolution: 2.01→2.06 Å / % possible obs: 98.9 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.604 / Num. measured all: 21759 / Num. unique obs: 4214 / CC1/2: 0.857 / Rpim(I) all: 0.288 / Rrim(I) all: 0.672 / Χ2: 0.82 / Net I/σ(I) obs: 2.4

-
Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
PDB-REDOrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.01→44.36 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2806 2901 4.96 %RANDOM
Rwork0.2273 ---
obs0.2299 58510 98.88 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.01→44.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6461 0 40 143 6644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076649
X-RAY DIFFRACTIONf_angle_d0.9379024
X-RAY DIFFRACTIONf_dihedral_angle_d7.421920
X-RAY DIFFRACTIONf_chiral_restr0.0541005
X-RAY DIFFRACTIONf_plane_restr0.0081152
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.01-2.040.35551190.29282572X-RAY DIFFRACTION98
2.04-2.080.29781610.27582607X-RAY DIFFRACTION100
2.08-2.120.33151410.2662612X-RAY DIFFRACTION98
2.12-2.160.3081140.26712619X-RAY DIFFRACTION99
2.16-2.20.33511310.26042623X-RAY DIFFRACTION99
2.2-2.250.32891350.26662578X-RAY DIFFRACTION100
2.25-2.30.33831340.25882656X-RAY DIFFRACTION99
2.3-2.360.32071460.25282584X-RAY DIFFRACTION99
2.36-2.420.31461340.24652627X-RAY DIFFRACTION99
2.42-2.490.29841430.25512644X-RAY DIFFRACTION99
2.49-2.570.31231480.26652587X-RAY DIFFRACTION99
2.57-2.670.34121230.26782669X-RAY DIFFRACTION99
2.67-2.770.38351400.26622672X-RAY DIFFRACTION99
2.77-2.90.29981430.26262581X-RAY DIFFRACTION98
2.9-3.050.31871200.25322684X-RAY DIFFRACTION99
3.05-3.240.28781400.25942694X-RAY DIFFRACTION99
3.24-3.490.27611340.22922656X-RAY DIFFRACTION98
3.49-3.840.24641410.21142677X-RAY DIFFRACTION99
3.84-4.40.26671470.18462676X-RAY DIFFRACTION99
4.4-5.540.20541460.15672710X-RAY DIFFRACTION98
5.54-44.360.2211610.19182881X-RAY DIFFRACTION99

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more