[English] 日本語
Yorodumi
- PDB-6o8d: Anti-CD28xCD3 CODV Fab bound to CD28 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6o8d
TitleAnti-CD28xCD3 CODV Fab bound to CD28
Components
  • Anti-CD28xCD3 CODV Fab Heavy chain
  • Anti-CD28xCD3 CODV Fab Light chain
  • T-cell-specific surface glycoprotein CD28
KeywordsIMMUNE SYSTEM / Multispecific antibody / cross-over dual variable immunoglobin / multifunctional biotherapeutic format / bispecific property / CODV / T cell activation
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 / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 co-stimulation ...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 / CD4-positive, alpha-beta T cell proliferation / positive regulation of isotype switching to IgG isotypes / negative thymic T cell selection / positive regulation of CD4-positive, alpha-beta T cell proliferation / CD28 co-stimulation / CD28 dependent Vav1 pathway / CD28 dependent PI3K/Akt signaling / positive regulation of interleukin-10 production / humoral immune response / immunological synapse / positive regulation of interleukin-4 production / positive regulation of viral genome replication / coreceptor activity / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-2 production / T cell activation / positive regulation of mitotic nuclear division / positive regulation of translation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of cytokine production / 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 / protease binding / transcription by RNA polymerase II / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
T-cell-specific surface glycoprotein CD28
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.547 Å
AuthorsLord, D.M. / Wei, R.R.
CitationJournal: To Be Published
Title: Trispecific antibodies enhance the therapeutic efficacy of tumor-directed T cells through T cell receptor co-stimulation
Authors: Wu, L. / Seung, E. / Xu, L. / Rao, E. / Lord, D.M. / Wei, R.R. / Cortez-Retamozo, V. / Ospina, B. / Posternak, V. / Ulinski, G. / Piepenhagen, P. / Francesconi, E. / El Murr, N. / Beil, C. / ...Authors: Wu, L. / Seung, E. / Xu, L. / Rao, E. / Lord, D.M. / Wei, R.R. / Cortez-Retamozo, V. / Ospina, B. / Posternak, V. / Ulinski, G. / Piepenhagen, P. / Francesconi, E. / El Murr, N. / Beil, C. / Dabdoubi, T. / Cameron, B. / Bertrand, T. / Ferrari, P. / Pouzieux, S. / Lemoine, C. / Prades, C. / Park, A. / Qiu, H. / Song, Z. / Zhang, B. / Sun, F. / Chiron, M. / Rao, S. / Radosevic, K. / Zhi-yong, Y. / Nabel, G.J.
History
DepositionMar 9, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 20, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: T-cell-specific surface glycoprotein CD28
L: Anti-CD28xCD3 CODV Fab Light chain
H: Anti-CD28xCD3 CODV Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,2515
Polymers90,6053
Non-polymers6462
Water0
1
C: T-cell-specific surface glycoprotein CD28
L: Anti-CD28xCD3 CODV Fab Light chain
H: Anti-CD28xCD3 CODV Fab Heavy chain
hetero molecules

C: T-cell-specific surface glycoprotein CD28
L: Anti-CD28xCD3 CODV Fab Light chain
H: Anti-CD28xCD3 CODV Fab Heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)182,50210
Polymers181,2106
Non-polymers1,2914
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)153.140, 60.139, 152.558
Angle α, β, γ (deg.)90.000, 104.040, 90.000
Int Tables number5
Space group name H-MC121

-
Components

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


Mass: 14617.518 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD28 / Production host: Homo sapiens (human) / References: UniProt: P10747
#2: Antibody Anti-CD28xCD3 CODV Fab Light chain


Mass: 36794.926 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody Anti-CD28xCD3 CODV Fab Heavy chain


Mass: 39192.723 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#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
#5: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.88 Å3/Da / Density % sol: 68.29 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 26% PEG3350, 0.75% myo-inositol, 0.263M potassium citrate tribasic monohydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9686 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 20, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 3.55→74.05 Å / Num. obs: 16611 / % possible obs: 99.8 % / Redundancy: 3.2 % / CC1/2: 0.635 / Rmerge(I) obs: 0.192 / Rpim(I) all: 0.133 / Rrim(I) all: 0.235 / Net I/σ(I): 4 / Num. measured all: 53137 / Scaling rejects: 697
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
3.55-3.643.30.717398711920.5670.4650.8581.599.7
15.88-74.052.50.1095352110.9370.0930.1449.899.2

-
Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.24data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: CODV-Fab: 6O89, CD28: 1YJD

6o89

1yjd


Resolution: 3.547→73.972 Å / SU ML: 0.71 / Cross valid method: THROUGHOUT / σ(F): 1.43 / Phase error: 42.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3561 1659 10.01 %
Rwork0.2723 14918 -
obs0.2807 16577 99.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 372.45 Å2 / Biso mean: 150.965 Å2 / Biso min: 38.2 Å2
Refinement stepCycle: final / Resolution: 3.547→73.972 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6141 0 42 0 6183
Biso mean--166.93 --
Num. residues----796
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.5472-3.65150.4571300.36991180131097
3.6515-3.76940.4511370.35731236137399
3.7694-3.90410.41191390.3541239137899
3.9041-4.06040.43631370.327412291366100
4.0604-4.24520.37591360.294612311367100
4.2452-4.4690.29431370.25212321369100
4.469-4.74890.29391390.238312411380100
4.7489-5.11550.32061410.23411264140599
5.1155-5.63010.36271350.26212281363100
5.6301-6.44440.34861420.279912611403100
6.4444-8.11770.37751400.286212701410100
8.1177-73.98820.33011460.22581307145399
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)
10.1077-0.037-0.06980.01160.0010.0173-1.0153-0.079-0.12910.08460.06630.33720.5696-0.2545-0.00061.4449-0.04310.39471.767-0.06481.3562-28.26193.581379.1596
22.97021.360.63621.41020.03510.2727-0.39820.01061.05410.79730.38540.72270.5575-0.9083-0.31322.70690.14360.32532.4566-0.03860.0385-37.80574.255275.3356
30.13040.07020.03090.1151-0.2020.3177-0.0922-0.0439-0.35170.2591-0.6071-0.4935-0.6527-1.1525-0.00081.5261-0.44060.24112.9922-0.03881.1832-30.79613.401865.4971
40.0790.04430.10450.02130.0720.07860.751-0.58330.3038-0.39490.51290.55151.6652-0.4726-0.00072.19420.06890.13822.6995-0.3241.4671-42.46051.046865.4351
50.1654-0.0007-0.02870.0025-0.0190.0264-0.23570.8347-0.33420.4274-0.54080.3539-0.07710.52170.0012.6532-0.9595-0.37193.88830.23711.5818-41.0142.763876.938
60.046-0.05420.01690.0228-0.0340.02290.49850.2092-0.3122-0.2550.2692-0.49890.92310.1340.00051.94040.0307-0.76421.6615-0.08981.9372-27.7076-9.347268.4025
74.2778-0.4788-0.30491.38391.32821.25250.4060.0079-0.5669-0.06180.4567-0.15530.09350.10990.16212.0435-0.3643-0.11242.1326-0.1295-0.6936-31.618.974269.7863
80.0727-0.0477-0.01320.02690.01410.01290.4544-0.37170.3610.3651-0.3259-1.0246-0.4-0.23520.00012.19380.0220.02281.9312-0.35291.8708-32.154719.246770.8759
90.0223-0.0368-0.01720.03950.01220.0111-0.25540.0349-0.87920.2536-0.17620.1010.4384-0.6810.0012.09650.35510.0441.8473-0.14791.7922-23.6663-1.507975.8962
100.2508-0.22871.21150.2458-0.26890.728-0.2623-0.6822-0.0278-0.0725-0.0291-0.01180.0417-0.1145-01.35050.0142-0.32081.1473-0.05671.0126-17.87649.387537.0337
113.74091.2473-3.03621.1484-1.19493.17190.0839-1.61960.86140.4116-0.4874-0.269-0.35790.6382-1.50071.3581-0.0779-0.45291.3706-0.22941.5107-40.13612.972639.1299
121.4993-0.01560.01140.21660.30181.2209-0.19490.0405-0.1999-0.22440.21310.32040.1552-0.03970.00020.50340.02210.11650.4388-0.02310.5816-45.59980.6764-7.221
130.64930.8549-0.51541.468-0.89770.45730.59520.49030.07210.6591-0.590.1744-1.1744-1.2953-0.00011.5632-0.045-0.29581.8013-0.11521.0691-32.313519.296145.8431
140.6228-0.2371-0.40570.0237-0.50320.648-0.1721-0.3567-0.3934-0.714-0.21830.0511-0.8502-0.2329-0.00990.64960.1764-0.16091.0306-0.08090.7974-22.313315.606526.5016
152.4565-1.3331.08021.1411-1.36862.3308-1.21960.34230.45860.4381-0.2382-1.102-1.1880.6307-0.30820.53410.03570.21730.61840.02240.5824-4.122514.659611.971
160.7334-0.32-0.86140.27220.08171.26010.1764-0.1699-0.24730.1274-0.05010.0756-0.02760.0818-0.00010.624-0.01510.03430.4491-0.06280.825-31.75088.3243-3.8091
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'C' and (resid 20 through 31 )C20 - 31
2X-RAY DIFFRACTION2chain 'C' and (resid 32 through 52 )C32 - 52
3X-RAY DIFFRACTION3chain 'C' and (resid 53 through 70 )C53 - 70
4X-RAY DIFFRACTION4chain 'C' and (resid 71 through 87 )C71 - 87
5X-RAY DIFFRACTION5chain 'C' and (resid 88 through 97 )C88 - 97
6X-RAY DIFFRACTION6chain 'C' and (resid 98 through 109 )C98 - 109
7X-RAY DIFFRACTION7chain 'C' and (resid 110 through 117 )C110 - 117
8X-RAY DIFFRACTION8chain 'C' and (resid 118 through 127 )C118 - 127
9X-RAY DIFFRACTION9chain 'C' and (resid 128 through 134 )C128 - 134
10X-RAY DIFFRACTION10chain 'L' and (resid 1 through 198 )L1 - 198
11X-RAY DIFFRACTION11chain 'L' and (resid 199 through 224 )L199 - 224
12X-RAY DIFFRACTION12chain 'L' and (resid 225 through 338 )L225 - 338
13X-RAY DIFFRACTION13chain 'H' and (resid 1 through 90 )H1 - 90
14X-RAY DIFFRACTION14chain 'H' and (resid 91 through 160 )H91 - 160
15X-RAY DIFFRACTION15chain 'H' and (resid 161 through 250 )H161 - 250
16X-RAY DIFFRACTION16chain 'H' and (resid 251 through 347 )H251 - 347

+
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