[English] 日本語
Yorodumi
- PDB-8w2v: Solution Structure of the CD28 hinge used in chimeric antigen rec... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8w2v
TitleSolution Structure of the CD28 hinge used in chimeric antigen receptor (CAR) T-cells
ComponentsT-cell-specific surface glycoprotein CD28
KeywordsIMMUNE SYSTEM / CAR-T / CD28 / immunotherapy / intrinsic disorder
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / regulatory T cell differentiation / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / positive regulation of isotype switching to IgG isotypes / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / CD28 co-stimulation / positive regulation of CD4-positive, alpha-beta T cell proliferation ...Nef mediated downregulation of CD28 cell surface expression / regulatory T cell differentiation / positive regulation of inflammatory response to antigenic stimulus / protein complex involved in cell adhesion / regulation of regulatory T cell differentiation / positive regulation of isotype switching to IgG isotypes / CD4-positive, alpha-beta T cell proliferation / negative thymic T cell selection / CD28 co-stimulation / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 dependent Vav1 pathway / positive regulation of interleukin-4 production / CD28 dependent PI3K/Akt signaling / humoral immune response / positive regulation of interleukin-10 production / immunological synapse / positive regulation of viral genome replication / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of mitotic nuclear division / T cell activation / positive regulation of cytokine production / positive regulation of translation / apoptotic signaling pathway / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / T cell receptor signaling pathway / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / transcription by RNA polymerase II / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / external side of plasma membrane / negative regulation of gene expression / positive regulation of gene expression / negative regulation of apoptotic process / protein kinase binding / cell surface / positive regulation of transcription by RNA polymerase II / identical protein binding / plasma membrane / cytosol
Similarity search - Function
T cell antigen CD28 / ICOS V-set domain / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsFolimonova, V. / Chen, X. / Walters, K.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1ZIABC011627 United States
CitationJournal: Commun Biol / Year: 2024
Title: CD28 hinge used in chimeric antigen receptor (CAR) T-cells exhibits local structure and conformational exchange amidst global disorder.
Authors: Folimonova, V. / Chen, X. / Negi, H. / Schwieters, C.D. / Li, J. / Byrd, R.A. / Taylor, N. / Youkharibache, P. / Walters, K.J.
History
DepositionFeb 21, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 11, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: T-cell-specific surface glycoprotein CD28


Theoretical massNumber of molelcules
Total (without water)4,3081
Polymers4,3081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: NMR Distance Restraints, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 50structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide T-cell-specific surface glycoprotein CD28 / TP44


Mass: 4308.027 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P10747

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D CON
1201isotropic42D 1H-15N HSQC
131isotropic23D HN(CA)CB
141isotropic23D CBCA(CO)NH
1191isotropic22D 1H-15N HSQC
2251isotropic42D 1H-15N HSQC
151isotropic23D HNCO
2261isotropic43D HNCO
161isotropic23D HN(CA)CO
2271isotropic43D HN(CA)CO
2301isotropic43D HNCO-COSY
1101isotropic23D HNCAN
192isotropic42D 1H-13C HSQC
2282isotropic22D 1H-13C HSQC
182isotropic43D 1H-13C NOESY
2292isotropic23D 1H-13C NOESY
1182isotropic12D 1H-13C HSQC
172isotropic13D 1H-13C CCH TOCSY
1112isotropic13D 1H-13C (H)CCH TOCSY
1213isotropic12D 1H-15N HSQC
1123isotropic12D CACO
1133isotropic13D CANCO
1174isotropic32D 1H-15N HSQC
2234isotropic22D 1H-15N HSQC
1144isotropic33D 1H-15N NOESY
2244isotropic23D 1H-15N NOESY
1155isotropic22D 1H-15N HSQC
1165isotropic23D HNHB

-
Sample preparation

Details
TypeSolution-IDContentsDetailsLabelSolvent system
solution10.5 mM [U-100% 13C; U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O15N, 13C-labeled CD28 hinge in 20 mM NaPO4 at pH 6.5, 50 mM NaCl, 2 mM dithiothreitol, 20 uM ZnSO4, 1mM pefabloc, 0.1% NaN3, and 95% H2O / 5% D2O15N, 13C-labeled CD28 hinge95% H2O/5% D2O
solution20.6 mM [U-100% 13C; U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 100% D2O15N, 13C-labeled CD28 hinge in 20 mM NaPO4 at pH 6.5, 50 mM NaCl, 2 mM dithiothreitol, 20 uM ZnSO4, 1mM pefabloc, 0.1% NaN3, and 100% D2O15N, 13C-labeled CD28 hinge100% D2O
solution30.45 mM [U-100% 13C; U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O15N, 13C-labeled CD28 hinge in 20 mM NaPO4 at pH 6.5, 50 mM NaCl, 2 mM dithiothreitol, 20 uM ZnSO4, 1mM pefabloc, 0.1% NaN3, and 95% H2O/ 95% D2O. 450 uM concentration.15N, 13C-labeled CD28 hinge95% H2O/5% D2O
solution40.4 mM [U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O15N-labeled CD28 hinge in 20 mM NaPO4 at pH 6.5, 50 mM NaCl, 2 mM dithiothreitol, 20 uM ZnSO4, 1mM pefabloc, 0.1% NaN3, and 95% H2O/ 95% D2O. 400 uM concentration.15N-labeled CD28 hinge95% H2O/5% D2O
solution50.28 mM [U-100% 15N] CD28 hinge, 20 mM sodium phosphate, 50 mM sodium chloride, 2 mM DTT, 20 uM zinc sulphate, 1 mM pefabloc, 0.1 % sodium azide, 95% H2O/5% D2O15N-labeled CD28 hinge in 20 mM NaPO4 at pH 6.5, 50 mM NaCl, 2 mM dithiothreitol, 20 uM ZnSO4, 1mM pefabloc, 0.1% NaN3, and 95% H2O/ 95% D2O. 280 uM concentration.15N-labeled CD28 hinge95% H2O/5% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.5 mMCD28 hinge[U-100% 13C; U-100% 15N]1
20 mMsodium phosphatenatural abundance1
50 mMsodium chloridenatural abundance1
2 mMDTTnatural abundance1
20 uMzinc sulphatenatural abundance1
1 mMpefablocnatural abundance1
0.1 %sodium azidenatural abundance1
0.6 mMCD28 hinge[U-100% 13C; U-100% 15N]2
20 mMsodium phosphatenatural abundance2
50 mMsodium chloridenatural abundance2
2 mMDTTnatural abundance2
20 uMzinc sulphatenatural abundance2
1 mMpefablocnatural abundance2
0.1 %sodium azidenatural abundance2
0.45 mMCD28 hinge[U-100% 13C; U-100% 15N]3
20 mMsodium phosphatenatural abundance3
50 mMsodium chloridenatural abundance3
2 mMDTTnatural abundance3
20 uMzinc sulphatenatural abundance3
1 mMpefablocnatural abundance3
0.1 %sodium azidenatural abundance3
0.4 mMCD28 hinge[U-100% 15N]4
20 mMsodium phosphatenatural abundance4
50 mMsodium chloridenatural abundance4
2 mMDTTnatural abundance4
20 uMzinc sulphatenatural abundance4
1 mMpefablocnatural abundance4
0.1 %sodium azidenatural abundance4
0.28 mMCD28 hinge[U-100% 15N]5
20 mMsodium phosphatenatural abundance5
50 mMsodium chloridenatural abundance5
2 mMDTTnatural abundance5
20 uMzinc sulphatenatural abundance5
1 mMpefablocnatural abundance5
0.1 %sodium azidenatural abundance5
Sample conditions
Conditions-IDIonic strengthLabelpHPressure (kPa)Temperature (K)
170 mM25 degree6.51 atm298 K
270 mM11 degree6.51 atm284 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AVANCE IIIBrukerAVANCE III7001
Bruker AVANCE IIIBrukerAVANCE III8002
Bruker AVANCE IIIBrukerAVANCE III8504
Bruker AVANCE IIIBrukerAVANCE III9003

-
Processing

NMR software
NameDeveloperClassification
TopSpinBruker Biospincollection
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
MddNMRV. Orekhov, V. Jaravine, M. Mayzel, K. Kazimierczukprocessing
XEASYBartels et al.peak picking
XEASYBartels et al.data analysis
TALOS+Yang Shen, Frank Delaglio, Gabriel Cornilescu & Ad Baxdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 7
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 50 / Conformers submitted total number: 25

+
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://pdbjlvh1.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