[English] 日本語
Yorodumi
- PDB-8s6z: CD28 in complex with the antibody Fab fragment AI3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8s6z
TitleCD28 in complex with the antibody Fab fragment AI3
Components
  • Heavy chain Fab fragment of AI3 antibody
  • Light chain of AI3 antibody
  • T-cell-specific surface glycoprotein CD28
KeywordsIMMUNE SYSTEM / Antibody / Complex / CD28
Function / homology
Function and homology information


Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / 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 / positive regulation of CD4-positive, alpha-beta T cell proliferation / Co-stimulation by CD28 ...Nef mediated downregulation of CD28 cell surface expression / positive regulation of inflammatory response to antigenic stimulus / regulatory T cell differentiation / 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 / positive regulation of CD4-positive, alpha-beta T cell proliferation / Co-stimulation by CD28 / CD28 dependent Vav1 pathway / positive regulation of interleukin-4 production / humoral immune response / positive regulation of interleukin-10 production / immunological synapse / CD28 dependent PI3K/Akt signaling / positive regulation of viral genome replication / positive regulation of T cell proliferation / coreceptor activity / T cell costimulation / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / T cell activation / positive regulation of translation / positive regulation of cytokine production / phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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
IMIDAZOLE / T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsMajocchi, S. / Giovanni, M. / Malinge, P. / Fischer, N. / Svensson, L.A. / Kelpsas, V. / Rose, N.C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Cancer Immunol Res / Year: 2025
Title: NI-3201 Is a Bispecific Antibody Mediating PD-L1-Dependent CD28 Co-stimulation on T Cells for Enhanced Tumor Control.
Authors: Majocchi, S. / Lloveras, P. / Nouveau, L. / Legrand, M. / Viandier, A. / Malinge, P. / Charreton, M. / Raymond, C. / Pace, E.A. / Millard, B.L. / Svensson, L.A. / Kelpsas, V. / Anceriz, N. / ...Authors: Majocchi, S. / Lloveras, P. / Nouveau, L. / Legrand, M. / Viandier, A. / Malinge, P. / Charreton, M. / Raymond, C. / Pace, E.A. / Millard, B.L. / Svensson, L.A. / Kelpsas, V. / Anceriz, N. / Salgado-Pires, S. / Daubeuf, B. / Magistrelli, G. / Gueneau, F. / Moine, V. / Masternak, K. / Shang, L. / Fischer, N. / Ferlin, W.G.
History
DepositionFeb 28, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 18, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 15, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 22, 2025Group: Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_assembly_gen
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _pdbx_struct_assembly_gen.asym_id_list
Revision 1.3Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heavy chain Fab fragment of AI3 antibody
B: Light chain of AI3 antibody
C: T-cell-specific surface glycoprotein CD28
D: Heavy chain Fab fragment of AI3 antibody
E: Light chain of AI3 antibody
F: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,83355
Polymers125,6816
Non-polymers5,15249
Water48627
1
A: Heavy chain Fab fragment of AI3 antibody
B: Light chain of AI3 antibody
C: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,55328
Polymers62,8403
Non-polymers2,71225
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Heavy chain Fab fragment of AI3 antibody
E: Light chain of AI3 antibody
F: T-cell-specific surface glycoprotein CD28
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,28027
Polymers62,8403
Non-polymers2,44024
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)76.874, 117.939, 145.719
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A
32A
42A
53A
63A

NCS domain segments:

Beg auth comp-ID: GLU / Beg label comp-ID: GLU / End auth comp-ID: PRO / End label comp-ID: PRO / Auth asym-ID: A / Label asym-ID: A

Dom-IDComponent-IDEns-IDAuth seq-IDLabel seq-ID
1111 - 2121 - 216
2111 - 2121 - 216
3221 - 2121 - 216
4221 - 2121 - 216
5331 - 1181 - 122
6331 - 1181 - 122

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6

-
Components

-
Protein , 1 types, 2 molecules CF

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


Mass: 15159.320 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD28 / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P10747

-
Antibody , 2 types, 4 molecules ADBE

#1: Antibody Heavy chain Fab fragment of AI3 antibody


Mass: 23468.174 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody Light chain of AI3 antibody


Mass: 24212.848 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 2 types, 10 molecules

#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#8: 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.: 9 / Source method: obtained synthetically / 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

-
Non-polymers , 4 types, 66 molecules

#5: Chemical
ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical...
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: Zn
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.63 Å3/Da / Density % sol: 53.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: Crystallization trials were set up using the CD28-AI3 Fab at 15.8 mg/mL in phosphate buffered saline (PBS) pH 7.4. Drops were set up using 100 nl protein and 100 nL reservoir solution ...Details: Crystallization trials were set up using the CD28-AI3 Fab at 15.8 mg/mL in phosphate buffered saline (PBS) pH 7.4. Drops were set up using 100 nl protein and 100 nL reservoir solution containing 200 mM zinc acetate, 0.1 M imidazole pH 8.0, 20% w/v PEG 3000.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.999873 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 22, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999873 Å / Relative weight: 1
ReflectionResolution: 3.05→91.843 Å / Num. obs: 25981 / % possible obs: 100 % / Redundancy: 10.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.243 / Rpim(I) all: 0.112 / Rrim(I) all: 0.268 / Χ2: 99.5 / Net I/σ(I): 8.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.63-91.678.90.05712790.9980.0260.063
3.05-3.2610.51.91246120.6020.8842.112

-
Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
REFMAC5.8.0425refinement
EDNAdata collection
XDSJun 30, 2023data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.05→91.843 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.906 / SU B: 57.088 / SU ML: 0.445 / Cross valid method: FREE R-VALUE / ESU R Free: 0.478
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2575 1327 5.118 %
Rwork0.1975 24599 -
all0.201 --
obs-25926 99.969 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 91.441 Å2
Baniso -1Baniso -2Baniso -3
1-7.175 Å2-0 Å2-0 Å2
2---5.263 Å2-0 Å2
3----1.912 Å2
Refinement stepCycle: LAST / Resolution: 3.05→91.843 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8507 0 251 27 8785
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0128939
X-RAY DIFFRACTIONr_bond_other_d0.0010.0168133
X-RAY DIFFRACTIONr_angle_refined_deg1.6871.81112147
X-RAY DIFFRACTIONr_angle_other_deg0.5861.73318854
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.84451104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.267530
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.976101414
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.97410358
X-RAY DIFFRACTIONr_chiral_restr0.0780.21381
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0210356
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022014
X-RAY DIFFRACTIONr_nbd_refined0.1940.21074
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.27353
X-RAY DIFFRACTIONr_nbtor_refined0.1770.24178
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.25062
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.2124
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0710.21
X-RAY DIFFRACTIONr_metal_ion_refined0.1370.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2180.232
X-RAY DIFFRACTIONr_nbd_other0.2560.285
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2480.25
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined0.1090.21
X-RAY DIFFRACTIONr_mcbond_it6.8646.844434
X-RAY DIFFRACTIONr_mcbond_other6.8636.8414434
X-RAY DIFFRACTIONr_mcangle_it10.1712.3115532
X-RAY DIFFRACTIONr_mcangle_other10.16912.3115533
X-RAY DIFFRACTIONr_scbond_it8.1177.3944505
X-RAY DIFFRACTIONr_scbond_other8.1167.3954506
X-RAY DIFFRACTIONr_scangle_it12.17213.3686615
X-RAY DIFFRACTIONr_scangle_other12.17113.3686616
X-RAY DIFFRACTIONr_lrange_it15.78486.36335237
X-RAY DIFFRACTIONr_lrange_other15.78586.36535229
X-RAY DIFFRACTIONr_ncsr_local_group_10.0570.056379
X-RAY DIFFRACTIONr_ncsr_local_group_20.0510.056725
X-RAY DIFFRACTIONr_ncsr_local_group_30.1130.053487
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.057220.0501
12AX-RAY DIFFRACTIONLocal ncs0.057220.0501
23AX-RAY DIFFRACTIONLocal ncs0.050910.0501
24AX-RAY DIFFRACTIONLocal ncs0.050910.0501
35AX-RAY DIFFRACTIONLocal ncs0.112810.0501
36AX-RAY DIFFRACTIONLocal ncs0.112810.0501
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
3.05-3.1290.365980.35917790.35918770.8780.8711000.361
3.129-3.2150.332950.32817460.32918410.8750.8941000.325
3.215-3.3080.311910.29116930.29217840.9270.931000.284
3.308-3.410.288850.25316530.25517380.9470.951000.239
3.41-3.5210.238750.21616160.21716910.9540.9661000.199
3.521-3.6450.285900.20415520.20816420.9240.971000.186
3.645-3.7820.237710.20514870.20615580.9550.9711000.181
3.782-3.9360.284610.17814670.18215290.9440.97699.93460.157
3.936-4.1110.249930.15713780.16214710.9590.9831000.136
4.111-4.3110.227960.1413100.14614060.970.9861000.124
4.311-4.5440.217660.12612700.13113360.9690.9891000.112
4.544-4.8190.195660.13911960.14212620.9710.9881000.126
4.819-5.150.191550.13311510.13612060.9730.991000.122
5.15-5.5610.208550.15710530.15911080.9740.9871000.143
5.561-6.090.236440.1749980.17710430.9640.98499.90410.159
6.09-6.8050.281570.1788790.1849360.9590.9791000.164
6.805-7.8510.297490.1928060.1978560.9520.97799.88320.181
7.851-9.5980.268350.1986860.2017220.9610.98199.86150.197
9.598-13.50.227230.2315480.2315710.9830.9781000.236
13.5-91.8430.41220.4653310.4613570.9240.88698.87960.51
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.6313-0.67320.51962.4504-1.78844.46270.05250.02590.0922-0.09230.10840.198-0.1274-0.3075-0.16090.05460.00360.0620.03370.00020.231418.9512-9.6231-27.0977
20.6774-0.3160.69211.1699-1.12171.9469-0.03860.01080.20140.2146-0.0826-0.1693-0.3260.10570.12110.1847-0.0054-0.00930.01830.03170.240533.5936-0.7706-31.9535
30.77910.8909-2.39976.2928-4.02117.79040.1095-0.0399-0.070.3055-0.238-0.2223-0.33470.24820.12860.16560.0733-0.05060.1139-0.05180.221633.1666-31.205910.9089
42.26111.2642-1.9932.6287-2.43873.06170.03570.19960.1666-0.06810.16820.30280.23-0.2274-0.20380.1990.0045-0.06880.0394-0.0110.19421.9338-22.3846-54.2006
51.23170.8283-0.5242.1393-1.21151.12640.07320.1495-0.1834-0.0836-0.2795-0.25610.14310.10850.20640.240.06390.02670.11180.01070.125932.7544-33.4232-45.7097
61.02910.0068-0.17355.7356-2.60376.0143-0.0788-0.20950.05820.0802-0.0988-0.13060.25690.32990.17760.04230.0160.05820.1255-0.06090.188549.5484-2.5876-84.6164
Refinement TLS groupSelection: ALL

+
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