6U9U | pdb_00006u9u

Structure of GM9_TH8seq732127 FAB


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 
    0.249 (Depositor), 0.251 (DCC) 
  • R-Value Work: 
    0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.210 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6U9U

This is version 1.4 of the entry. See complete history

Literature

Extensive dissemination and intraclonal maturation of HIV Env vaccine-induced B cell responses.

Phad, G.E.Pushparaj, P.Tran, K.Dubrovskaya, V.Adori, M.Martinez-Murillo, P.Vazquez Bernat, N.Singh, S.Dionne, G.O'Dell, S.Bhullar, K.Narang, S.Sorini, C.Villablanca, E.J.Sundling, C.Murrell, B.Mascola, J.R.Shapiro, L.Pancera, M.Martin, M.Corcoran, M.Wyatt, R.T.Karlsson Hedestam, G.B.

(2020) J Exp Medicine 217

  • DOI: https://doi.org/10.1084/jem.20191155
  • Primary Citation Related Structures: 
    6U3Z, 6U9U

  • PubMed Abstract: 

    Well-ordered HIV-1 envelope glycoprotein (Env) trimers are prioritized for clinical evaluation, and there is a need for an improved understanding about how elicited B cell responses evolve following immunization. To accomplish this, we prime-boosted rhesus macaques with clade C NFL trimers and identified 180 unique Ab lineages from ∼1,000 single-sorted Env-specific memory B cells. We traced all lineages in high-throughput heavy chain (HC) repertoire (Rep-seq) data generated from multiple immune compartments and time points and expressed several as monoclonal Abs (mAbs). Our results revealed broad dissemination and high levels of somatic hypermutation (SHM) of most lineages, including tier 2 virus neutralizing lineages, following boosting. SHM was highest in the Ab complementarity determining regions (CDRs) but also surprisingly high in the framework regions (FRs), especially FR3. Our results demonstrate the capacity of the immune system to affinity-mature large numbers of Env-specific B cell lineages simultaneously, supporting the use of regimens consisting of repeated boosts to improve each Ab, even those belonging to less expanded lineages.


  • Organizational Affiliation
    • Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden.

Macromolecule Content 

  • Total Structure Weight: 47.63 kDa 
  • Atom Count: 3,409 
  • Modeled Residue Count: 430 
  • Deposited Residue Count: 438 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GM9_TH8seq732127 FAB heavy chainA [auth H]224Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GM9_TH8seq732127 FAB light chainB [auth L]214Homo sapiensMutation(s): 0 

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth H],
L
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
FMT

Query on FMT



Download:Ideal Coordinates CCD File
E [auth H],
K [auth L]
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth H]
D [auth H]
G [auth L]
H [auth L]
I [auth L]
C [auth H],
D [auth H],
G [auth L],
H [auth L],
I [auth L],
J [auth L]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free:  0.249 (Depositor), 0.251 (DCC) 
  • R-Value Work:  0.208 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.210 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 147.709α = 90
b = 147.709β = 90
c = 63.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesP01 AI104722

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-06
    Type: Initial release
  • Version 1.1: 2019-11-20
    Changes: Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-25
    Changes: Database references
  • Version 1.4: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary