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- PDB-6o8d: Anti-CD28xCD3 CODV Fab bound to CD28 -

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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 / 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 / coreceptor activity / T cell costimulation / positive regulation of T cell proliferation / positive regulation of interleukin-2 production / positive regulation of mitotic nuclear division / T cell activation / positive regulation of translation / positive regulation of cytokine production / apoptotic signaling pathway / phosphatidylinositol 3-kinase/protein kinase B signal transduction / 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 / cell surface receptor signaling pathway / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of gene expression / external side of plasma membrane / positive regulation of gene expression / protein kinase binding / negative regulation of apoptotic process / 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 / Immunoglobulins / 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
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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
Water00
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

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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


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
Has protein modificationY

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Experimental details

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Experiment

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

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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

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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

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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

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