[English] 日本語
Yorodumi
- PDB-6xrj: Crystal structure of the disulfide linked DH717.1 Fab dimer, deri... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6xrj
TitleCrystal structure of the disulfide linked DH717.1 Fab dimer, derived from a macaque HIV-1 vaccine-induced Env glycan-reactive neutralizing antibody B cell lineage
Components
  • DH717.1 heavy chain Fab fragment
  • DH717.1 light chain Fab fragment
KeywordsIMMUNE SYSTEM / Fab-dimerized / glycan-reactive / antibodies / HIV
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.15 Å
AuthorsManne, K. / Nicely, N.I. / Acharya, P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI145687 United States
Citation
Journal: Cell / Year: 2021
Title: Fab-dimerized glycan-reactive antibodies are a structural category of natural antibodies.
Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler ...Authors: Wilton B Williams / R Ryan Meyerhoff / R J Edwards / Hui Li / Kartik Manne / Nathan I Nicely / Rory Henderson / Ye Zhou / Katarzyna Janowska / Katayoun Mansouri / Sophie Gobeil / Tyler Evangelous / Bhavna Hora / Madison Berry / A Yousef Abuahmad / Jordan Sprenz / Margaret Deyton / Victoria Stalls / Megan Kopp / Allen L Hsu / Mario J Borgnia / Guillaume B E Stewart-Jones / Matthew S Lee / Naomi Bronkema / M Anthony Moody / Kevin Wiehe / Todd Bradley / S Munir Alam / Robert J Parks / Andrew Foulger / Thomas Oguin / Gregory D Sempowski / Mattia Bonsignori / Celia C LaBranche / David C Montefiori / Michael Seaman / Sampa Santra / John Perfect / Joseph R Francica / Geoffrey M Lynn / Baptiste Aussedat / William E Walkowicz / Richard Laga / Garnett Kelsoe / Kevin O Saunders / Daniela Fera / Peter D Kwong / Robert A Seder / Alberto Bartesaghi / George M Shaw / Priyamvada Acharya / Barton F Haynes /
Abstract: Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) ...Natural antibodies (Abs) can target host glycans on the surface of pathogens. We studied the evolution of glycan-reactive B cells of rhesus macaques and humans using glycosylated HIV-1 envelope (Env) as a model antigen. 2G12 is a broadly neutralizing Ab (bnAb) that targets a conserved glycan patch on Env of geographically diverse HIV-1 strains using a unique heavy-chain (V) domain-swapped architecture that results in fragment antigen-binding (Fab) dimerization. Here, we describe HIV-1 Env Fab-dimerized glycan (FDG)-reactive bnAbs without V-swapped domains from simian-human immunodeficiency virus (SHIV)-infected macaques. FDG Abs also recognized cell-surface glycans on diverse pathogens, including yeast and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike. FDG precursors were expanded by glycan-bearing immunogens in macaques and were abundant in HIV-1-naive humans. Moreover, FDG precursors were predominately mutated IgMIgDCD27, thus suggesting that they originated from a pool of antigen-experienced IgM or marginal zone B cells.
#1: Journal: bioRxiv / Year: 2020
Title: Fab-dimerized glycan-reactive antibodies neutralize HIV and are prevalent in humans and rhesus macaques
Authors: Acharya, P. / Williams, W. / Henderson, R. / Janowska, K. / Manne, K. / Parks, R. / Deyton, M. / Sprenz, J. / Stalls, V. / Kopp, M. / Mansouri, K. / Edwards, R.J. / Meyerhoff, R.R. / Oguin, ...Authors: Acharya, P. / Williams, W. / Henderson, R. / Janowska, K. / Manne, K. / Parks, R. / Deyton, M. / Sprenz, J. / Stalls, V. / Kopp, M. / Mansouri, K. / Edwards, R.J. / Meyerhoff, R.R. / Oguin, T. / Sempowski, G. / Saunders, K. / Haynes, B.F.
History
DepositionJul 13, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jun 9, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.journal_id_ISSN / _database_2.pdbx_DOI ..._citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DH717.1 heavy chain Fab fragment
B: DH717.1 light chain Fab fragment
C: DH717.1 heavy chain Fab fragment
D: DH717.1 light chain Fab fragment
E: DH717.1 heavy chain Fab fragment
F: DH717.1 light chain Fab fragment
H: DH717.1 heavy chain Fab fragment
L: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)185,3028
Polymers185,3028
Non-polymers00
Water00
1
A: DH717.1 heavy chain Fab fragment
B: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area19320 Å2
MethodPISA
2
C: DH717.1 heavy chain Fab fragment
D: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-25 kcal/mol
Surface area20800 Å2
MethodPISA
3
E: DH717.1 heavy chain Fab fragment
F: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-21 kcal/mol
Surface area20720 Å2
MethodPISA
4
H: DH717.1 heavy chain Fab fragment
L: DH717.1 light chain Fab fragment


Theoretical massNumber of molelcules
Total (without water)46,3252
Polymers46,3252
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3840 Å2
ΔGint-27 kcal/mol
Surface area20700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)201.587, 201.587, 154.327
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Space group name HallP4cw2c
Symmetry operation#1: x,y,z
#2: -y,x,z+3/4
#3: y,-x,z+1/4
#4: x,-y,-z+1/2
#5: -x,y,-z
#6: -x,-y,z+1/2
#7: y,x,-z+1/4
#8: -y,-x,-z+3/4
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
12
22
32
42

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLNGLNSERSERchain 'A'AA1 - 1381 - 138
121GLUGLUILEILEchain 'A'AA144 - 224144 - 224
211GLNGLNSERSER(chain 'C' and (resid 1 through 138 or resid 144 through 224))CC1 - 1381 - 138
221GLUGLUILEILE(chain 'C' and (resid 1 through 138 or resid 144 through 224))CC144 - 224144 - 224
311GLNGLNSERSER(chain 'E' and (resid 1 through 138 or resid 144 through 224))EE1 - 1381 - 138
321GLUGLUILEILE(chain 'E' and (resid 1 through 138 or resid 144 through 224))EE144 - 224144 - 224
411GLNGLNSERSER(chain 'H' and (resid 1 through 138 or resid 144 through 224))HG1 - 1381 - 138
421GLUGLUILEILE(chain 'H' and (resid 1 through 138 or resid 144 through 224))HG144 - 224144 - 224
112ALAALAPROPROchain 'B'BB3 - 2121 - 210
212ALAALAPROPROchain 'D'DD3 - 2121 - 210
312ALAALAPROPROchain 'F'FF3 - 2121 - 210
412ALAALAPROPROchain 'L'LH3 - 2121 - 210

NCS ensembles :
ID
1
2

-
Components

#1: Antibody
DH717.1 heavy chain Fab fragment


Mass: 24092.014 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
DH717.1 light chain Fab fragment


Mass: 22233.449 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.93 %
Crystal growTemperature: 295.15 K / Method: vapor diffusion, sitting drop / pH: 3.5 / Details: 0.1M Citric acid pH3.5, 14% PEG 1000

-
Data collection

DiffractionMean temperature: 193.15 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 3, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.147→41.71 Å / Num. obs: 55412 / % possible obs: 99.72 % / Redundancy: 9 % / Biso Wilson estimate: 82.54 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.166 / Net I/σ(I): 13.4
Reflection shellResolution: 3.147→3.26 Å / Redundancy: 9.6 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 5393 / CC1/2: 0.525 / % possible all: 98.94

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ukn

5ukn


Resolution: 3.15→41.71 Å / SU ML: 0.305 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.5962
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2822 1999 3.61 %1999
Rwork0.245 53413 --
obs0.2464 55412 99.79 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 113.53 Å2
Refinement stepCycle: LAST / Resolution: 3.15→41.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12965 0 0 0 12965
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012113260
X-RAY DIFFRACTIONf_angle_d2.033818086
X-RAY DIFFRACTIONf_chiral_restr0.11192077
X-RAY DIFFRACTIONf_plane_restr0.01262322
X-RAY DIFFRACTIONf_dihedral_angle_d16.66044680
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.15-3.230.34981380.32123683X-RAY DIFFRACTION98.53
3.23-3.310.29961400.29773776X-RAY DIFFRACTION99.95
3.31-3.410.33031410.28023769X-RAY DIFFRACTION100
3.41-3.520.29331420.26593772X-RAY DIFFRACTION99.95
3.52-3.650.30261400.2723767X-RAY DIFFRACTION100
3.65-3.790.29441430.26453790X-RAY DIFFRACTION99.9
3.79-3.960.27351410.25323783X-RAY DIFFRACTION99.7
3.97-4.170.31681420.23273792X-RAY DIFFRACTION99.97
4.17-4.440.25211410.2183789X-RAY DIFFRACTION99.97
4.44-4.780.24741430.20933820X-RAY DIFFRACTION100
4.78-5.260.22441440.22093836X-RAY DIFFRACTION99.92
5.26-6.010.32421450.24033866X-RAY DIFFRACTION100
6.02-7.570.26771450.26483895X-RAY DIFFRACTION99.7
7.57-41.710.29251540.2384075X-RAY DIFFRACTION99.41

+
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