[English] 日本語
Yorodumi
- PDB-8gye: Crystal Structure of the 4-1BB in complex with ZG033 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8gye
TitleCrystal Structure of the 4-1BB in complex with ZG033 Fab
Components
  • Tumor necrosis factor receptor superfamily member 9
  • ZG033 Fab H chain
  • ZG033 Fab L chain
KeywordsIMMUNE SYSTEM / Unique epitope / Binding affinity / intermediate level of activation of T cells
Function / homology
Function and homology information


TNFs bind their physiological receptors / regulation of immature T cell proliferation in thymus / signaling receptor activity / regulation of cell population proliferation / external side of plasma membrane / negative regulation of cell population proliferation / apoptotic process / plasma membrane
Similarity search - Function
Tumour necrosis factor receptor 9 / Tumour necrosis factor receptor 9, N-terminal / TNFR/NGFR family cysteine-rich region domain profile. / TNFR/NGFR cysteine-rich region / TNFR/NGFR family cysteine-rich region signature. / Tumor necrosis factor receptor / nerve growth factor receptor repeats. / TNFR/NGFR cysteine-rich region / Growth factor receptor cysteine-rich domain superfamily
Similarity search - Domain/homology
Tumor necrosis factor receptor superfamily member 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsZhu, M. / Cheng, L.S. / Gao, Y.
Funding support China, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)U1632124 China
National Natural Science Foundation of China (NSFC)31621002 China
National Natural Science Foundation of China (NSFC)31270770 China
Ministry of Science and Technology (MoST, China)2017YFA0503600 China
Ministry of Science and Technology (MoST, China)2017YFA0504903 China
CitationJournal: To Be Published
Title: Crystal Structure of the 4-1BB in complex with ZG033 Fab
Authors: Zhu, M. / Cheng, L.S. / Gao, Y.
History
DepositionSep 22, 2022Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 27, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Revision 1.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tumor necrosis factor receptor superfamily member 9
D: Tumor necrosis factor receptor superfamily member 9
B: ZG033 Fab H chain
C: ZG033 Fab L chain
E: ZG033 Fab H chain
F: ZG033 Fab L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8669
Polymers130,3316
Non-polymers5353
Water2,306128
1
A: Tumor necrosis factor receptor superfamily member 9
E: ZG033 Fab H chain
F: ZG033 Fab L chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4795
Polymers65,1663
Non-polymers3132
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ZG033 Fab H chain
C: ZG033 Fab L chain

D: Tumor necrosis factor receptor superfamily member 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3874
Polymers65,1663
Non-polymers2211
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_545x,y-1,z1
Unit cell
Length a, b, c (Å)60.021, 65.913, 83.643
Angle α, β, γ (deg.)90.000, 82.495, 74.822
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z

-
Components

-
Antibody , 2 types, 4 molecules BECF

#2: Antibody ZG033 Fab H chain


Mass: 23180.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi 293F / Cell line (production host): Expi 293F / Production host: Homo sapiens (human)
#3: Antibody ZG033 Fab L chain


Mass: 23442.953 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi 293F / Cell line (production host): Expi 293F / Production host: Homo sapiens (human)

-
Protein / Sugars , 2 types, 4 molecules AD

#1: Protein Tumor necrosis factor receptor superfamily member 9 / 4-1BB ligand receptor / CDw137 / T-cell antigen 4-1BB homolog / T-cell antigen ILA


Mass: 18541.754 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Expi 293F / Gene: TNFRSF9, CD137, ILA / Cell line (production host): Expi 293F / Production host: Homo sapiens (human) / Strain (production host): Expi 293F / References: UniProt: Q07011
#4: 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.: 2 / 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 , 2 types, 129 molecules

#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 128 / 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: 2.43 Å3/Da / Density % sol: 49.34 %
Crystal growTemperature: 287 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 18% (w/v) PEG4000, 0.1M Tris pH8.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.3→19.91 Å / Num. obs: 52988 / % possible obs: 97.19 % / Redundancy: 3.5 % / Biso Wilson estimate: 46.08 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.37 Å / Rmerge(I) obs: 0.821 / Num. unique obs: 5290

-
Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4EDW

4edw


Resolution: 2.3→19.91 Å / SU ML: 0.3524 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 36.2471 / Stereochemistry target values: CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2766 2593 4.9 %
Rwork0.2222 50357 -
obs0.2248 52950 97.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 62.23 Å2
Refinement stepCycle: LAST / Resolution: 2.3→19.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8499 0 34 128 8661
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00188739
X-RAY DIFFRACTIONf_angle_d0.533111889
X-RAY DIFFRACTIONf_chiral_restr0.04181343
X-RAY DIFFRACTIONf_plane_restr0.00371524
X-RAY DIFFRACTIONf_dihedral_angle_d14.16475314
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.340.42351460.3632628X-RAY DIFFRACTION97.37
2.34-2.390.46461280.37182674X-RAY DIFFRACTION96.89
2.39-2.440.40031320.35142657X-RAY DIFFRACTION97.52
2.44-2.490.43681450.34212615X-RAY DIFFRACTION97.42
2.49-2.550.4021410.30992686X-RAY DIFFRACTION97.38
2.55-2.610.34161260.31272672X-RAY DIFFRACTION97.8
2.61-2.680.35031510.29182618X-RAY DIFFRACTION97.47
2.68-2.760.34331390.28932677X-RAY DIFFRACTION97.78
2.76-2.850.32521410.27332683X-RAY DIFFRACTION97.95
2.85-2.950.32851430.26522635X-RAY DIFFRACTION97.71
2.95-3.070.33731210.2532646X-RAY DIFFRACTION97.57
3.07-3.210.31061400.25012673X-RAY DIFFRACTION97.81
3.21-3.370.26461280.2362652X-RAY DIFFRACTION97.41
3.37-3.580.27731270.22172659X-RAY DIFFRACTION97.04
3.58-3.860.26641370.21542646X-RAY DIFFRACTION97.14
3.86-4.240.2781500.18972632X-RAY DIFFRACTION97.41
4.24-4.850.20061200.1632670X-RAY DIFFRACTION97.35
4.85-6.080.21081440.17062609X-RAY DIFFRACTION96.19
6.08-19.910.2091340.17182625X-RAY DIFFRACTION96.2

+
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