[English] 日本語
Yorodumi
- PDB-8gab: Crystal structure of CTLA-4 in complex with a high affinity CTLA-... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gab
TitleCrystal structure of CTLA-4 in complex with a high affinity CTLA-4 binder
Components
  • CTLA-4 binder
  • Cytotoxic T-lymphocyte protein 4
KeywordsDE NOVO PROTEIN/Immune System / CTLA-4 / De novo protein design / high affinity binder / IMMUNE SYSTEM / DE NOVO PROTEIN-Immune System complex
Function / homology
Function and homology information


protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response ...protein complex involved in cell adhesion / negative regulation of regulatory T cell differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / clathrin-coated endocytic vesicle / CTLA4 inhibitory signaling / negative regulation of B cell proliferation / negative regulation of T cell proliferation / B cell receptor signaling pathway / T cell receptor signaling pathway / adaptive immune response / immune response / positive regulation of apoptotic process / external side of plasma membrane / DNA damage response / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane
Similarity search - Function
Cytotoxic T-lymphocyte antigen 4 / Cytotoxic T-lymphocyte protein 4/CD28 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
: / Cytotoxic T-lymphocyte protein 4
Similarity search - Component
Biological speciessynthetic construct (others)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.72 Å
AuthorsYang, W. / Almo, S.C. / Ghosh, A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD020068 United States
CitationJournal: To Be Published
Title: Crystal structure of a high affinity CTLA-4 binder
Authors: Yang, W. / Almo, S.C. / Ghosh, A. / Baker, D.
History
DepositionFeb 22, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CTLA-4 binder
B: Cytotoxic T-lymphocyte protein 4
C: CTLA-4 binder
D: Cytotoxic T-lymphocyte protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6475
Polymers52,6084
Non-polymers391
Water905
1
A: CTLA-4 binder
B: Cytotoxic T-lymphocyte protein 4


Theoretical massNumber of molelcules
Total (without water)26,3042
Polymers26,3042
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-13 kcal/mol
Surface area10730 Å2
MethodPISA
2
C: CTLA-4 binder
D: Cytotoxic T-lymphocyte protein 4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,3433
Polymers26,3042
Non-polymers391
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-13 kcal/mol
Surface area10580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)175.749, 33.604, 74.474
Angle α, β, γ (deg.)90.00, 101.15, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein CTLA-4 binder


Mass: 12793.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Plasmid: pET29 / Production host: Escherichia coli BL21(DE3) (bacteria)
#2: Protein Cytotoxic T-lymphocyte protein 4 / Cytotoxic T-lymphocyte-associated antigen 4 / CTLA-4


Mass: 13510.340 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CTLA4, CD152 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16410
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.05 Å3/Da / Density % sol: 40.02 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 22% (w/v) PEG 3350 and 0.2 M KCl

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.72→25 Å / Num. obs: 11876 / % possible obs: 99.8 % / Redundancy: 3.7 % / CC1/2: 0.99 / CC star: 0.99 / Rmerge(I) obs: 0.087 / Net I/σ(I): 10.35
Reflection shellResolution: 2.72→2.82 Å / Rmerge(I) obs: 0.89 / Mean I/σ(I) obs: 2.08 / Num. unique obs: 1237 / CC1/2: 0.87 / CC star: 0.88

-
Processing

Software
NameVersionClassification
Aimlessdata scaling
autoPROCdata reduction
PHASER2.8.3phasing
PHENIX1.20.1_4487refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.72→24.95 Å / SU ML: 0.48 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 31.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.292 548 4.62 %
Rwork0.2471 --
obs0.2496 11862 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.72→24.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3458 0 1 5 3464
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063514
X-RAY DIFFRACTIONf_angle_d1.3274764
X-RAY DIFFRACTIONf_dihedral_angle_d13.598476
X-RAY DIFFRACTIONf_chiral_restr0.055564
X-RAY DIFFRACTIONf_plane_restr0.03610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.72-2.990.3741480.35392751X-RAY DIFFRACTION99
2.99-3.420.35311260.29652805X-RAY DIFFRACTION100
3.42-4.310.33241150.25062846X-RAY DIFFRACTION100
4.31-24.950.25781590.21422912X-RAY DIFFRACTION100
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)
19.91993.4230.72188.5953-2.12038.4669-0.2906-0.4579-0.33012.41640.90970.4517-0.8975-1.015-0.12840.8592-0.00760.09790.6038-0.02680.7528-31.583-8.9065.424
24.77122.98580.32412.7420.69237.2808-1.05940.20380.0696-3.04980.09121.29520.4037-1.32160.28980.73880.01060.01570.7396-0.05720.7488-29.411-6.284-4.816
34.6836-4.4193-3.63738.2101-3.14867.7111-0.6886-0.0965-0.26250.00430.68570.29390.0366-0.0460.12960.7052-0.0606-0.01230.5724-0.05190.6943-22.336-6.7890.835
43.3284-2.84281.58498.8278-1.37895.6719-1.08291.75080.462-2.55970.7657-1.0364-1.64051.33270.20280.77260.01080.13570.64910.09490.7656-16.455-4.112-7.127
58.03450.10340.90266.5674-1.51337.81180.0449-0.0661-0.4021-1.37780.1215-0.9926-0.10680.7273-0.37520.81790.03270.09920.6488-0.04690.8179-11.178-5.261.574
63.232-2.61133.81652.2754-3.78614.6365-0.253-1.01480.71430.25010.255-0.5072-0.91380.84430.42670.654-0.0591-0.03671.4101-0.31330.7121-3.759-8.96321.578
75.6980.70883.26847.1443-2.26439.74730.0254-1.22990.1040.0719-0.02570.35740.8054-0.2659-0.17890.79770.0176-0.00390.6094-0.13510.529-12.311-11.58312.796
84.8416-0.11934.84735.04811.05224.8163-2.60921.1158-0.57921.78651.4661-0.69731.8853-0.80870.52741.3602-0.02530.25551.23030.45081.3748-11.749-21.58816.421
95.6173-1.4835-0.98123.47990.21074.4009-0.3694-1.26550.37430.08830.2227-0.13020.0320.48940.08120.7073-0.04010.01220.59980.01860.5576-8.53-10.99315.998
1010.17240.637-1.58142.30621.66465.7612-0.15230.9655-0.2463-0.23891.1585-1.8415-0.68730.744-0.78870.87350.00450.03030.58610.02820.4449-39.4231.79213.127
118.86210.02551.98243.1459-0.40997.9040.0280.43280.3874-1.36791.25072.2091-0.3104-0.6582-1.00420.63990.11590.01680.89270.04490.6122-49.824-0.74714.229
129.7022.8685-0.73934.2506-0.5884.69760.2661-0.53050.0255-1.6597-0.1146-1.54510.21440.2344-0.39070.53380.0408-0.00730.49470.00740.3713-44.553-0.84921.659
133.54951.97632.44143.07220.02367.0262-0.2364-1.2737-1.22470.35641.41362.5230.256-1.4009-0.64380.5485-0.040.00111.00270.17050.8853-52.468-4.18826.928
148.3425-2.50021.75535.70036.22269.67850.2291-1.42860.93080.68420.7365-0.2287-0.474-1.1289-1.26230.6429-0.1330.10150.67750.13410.5701-44.194-2.69732.894
158.8363-0.29455.34926.35481.11714.38850.2909-0.47540.24471.4130.1417-1.15330.8321.4192-0.68650.8174-0.0228-0.33130.70190.00921.0246-25.757-0.1441.95
166.46315.4777-4.6599.3096-5.83684.87380.15043.71980.4316-5.32370.48552.11411.34380.74111.15781.4322-0.04980.35961.7934-0.08731.2962-24.9112.46322.294
176.4657-2.66582.97433.0417-1.63942.7845-0.4281-0.43681.1152-1.36074.40074.14871.7967-5.4865-0.5480.7371-0.2323-0.14181.0441-0.12920.7759-37.5970.63637.291
184.03423.7124-0.91484.5887-1.50533.2332-0.032-1.36512.1096-1.03920.47751.95760.10130.13060.00840.9840.02410.11740.74750.09010.9077-35.077.18434.339
196.2279-3.54.92044.6543-1.87623.9545-2.0442-0.54571.4885-1.33751.7861-1.58680.65441.8405-0.25271.5677-0.3694-0.08690.9635-0.16541.0615-31.05613.04534.796
203.6039-2.9681-1.71543.91661.90227.8486-1.17771.4561-1.24230.46270.6081-2.75120.62982.0960.46230.8881-0.35920.10761.1215-0.05871.0768-24.4226.78136.075
214.470.32512.72337.89082.53565.92740.5757-1.0584-0.52551.00730.3636-0.13320.5555-0.7125-1.16090.4594-0.0748-0.0060.83020.10160.6945-33.5831.09434.566
226.2929-0.0764-3.83325.55117.35152.0121-0.10471.296-0.57543.1038-1.6931-0.50233.0149-1.31560.0221.48130.0364-0.421.26350.21331.1286-29.564-2.70750.146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 2:22 )A2 - 22
2X-RAY DIFFRACTION2( CHAIN A AND RESID 23:42 )A23 - 42
3X-RAY DIFFRACTION3( CHAIN A AND RESID 43:65 )A43 - 65
4X-RAY DIFFRACTION4( CHAIN A AND RESID 66:85 )A66 - 85
5X-RAY DIFFRACTION5( CHAIN A AND RESID 86:105 )A86 - 105
6X-RAY DIFFRACTION6( CHAIN B AND RESID 3:24 )B3 - 24
7X-RAY DIFFRACTION7( CHAIN B AND RESID 25:55 )B25 - 55
8X-RAY DIFFRACTION8( CHAIN B AND RESID 56:67 )B56 - 67
9X-RAY DIFFRACTION9( CHAIN B AND RESID 68:117 )B68 - 117
10X-RAY DIFFRACTION10( CHAIN C AND RESID 2:22 )C2 - 22
11X-RAY DIFFRACTION11( CHAIN C AND RESID 23:42 )C23 - 42
12X-RAY DIFFRACTION12( CHAIN C AND RESID 43:65 )C43 - 65
13X-RAY DIFFRACTION13( CHAIN C AND RESID 66:86 )C66 - 86
14X-RAY DIFFRACTION14( CHAIN C AND RESID 87:104 )C87 - 104
15X-RAY DIFFRACTION15( CHAIN D AND RESID 3:24 )D3 - 24
16X-RAY DIFFRACTION16( CHAIN D AND RESID 25:32 )D25 - 32
17X-RAY DIFFRACTION17( CHAIN D AND RESID 33:45 )D33 - 45
18X-RAY DIFFRACTION18( CHAIN D AND RESID 46:55 )D46 - 55
19X-RAY DIFFRACTION19( CHAIN D AND RESID 56:67 )D56 - 67
20X-RAY DIFFRACTION20( CHAIN D AND RESID 68:81 )D68 - 81
21X-RAY DIFFRACTION21( CHAIN D AND RESID 82:111 )D82 - 111
22X-RAY DIFFRACTION22( CHAIN D AND RESID 112:117 )D112 - 117

+
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://pdbjlc1.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