[English] 日本語
Yorodumi
- PDB-8cx3: Crystal structure of full-length mesothelin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8cx3
TitleCrystal structure of full-length mesothelin
ComponentsIsoform 4 of Mesothelin
KeywordsCELL ADHESION / Mesothelin
Function / homology
Function and homology information


Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region ...Post-translational modification: synthesis of GPI-anchored proteins / side of membrane / cell-matrix adhesion / Post-translational protein phosphorylation / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / cell adhesion / endoplasmic reticulum lumen / Golgi apparatus / cell surface / extracellular region / membrane / plasma membrane
Similarity search - Function
Mesothelin / Stereocilin-related / Mesothelin
Similarity search - Domain/homology
PHOSPHATE ION / Mesothelin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.609 Å
AuthorsZhan, J. / Esser, L. / Xia, D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: Cancer Res Commun / Year: 2023
Title: Structures of Cancer Antigen Mesothelin and Its Complexes with Therapeutic Antibodies.
Authors: Zhan, J. / Lin, D. / Watson, N. / Esser, L. / Tang, W.K. / Zhang, A. / Liu, X. / Hassan, R. / Gleinich, A. / Shajahan, A. / Azadi, P. / Pastan, I. / Xia, D.
History
DepositionMay 19, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2023Group: Database references / Refinement description
Category: citation / citation_author ...citation / citation_author / refine_ls_restr / refine_ls_restr_ncs / struct_ncs_dom / struct_ncs_dom_lim / struct_ncs_ens
Item: _citation.journal_abbrev / _citation.journal_id_ISSN ..._citation.journal_abbrev / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Nov 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: Isoform 4 of Mesothelin
B: Isoform 4 of Mesothelin
C: Isoform 4 of Mesothelin
D: Isoform 4 of Mesothelin
E: Isoform 4 of Mesothelin
F: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)214,87327
Polymers211,5676
Non-polymers3,30621
Water00
1
A: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6704
Polymers35,2611
Non-polymers4083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7645
Polymers35,2611
Non-polymers5034
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6704
Polymers35,2611
Non-polymers4083
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8734
Polymers35,2611
Non-polymers6113
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7675
Polymers35,2611
Non-polymers5064
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Isoform 4 of Mesothelin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,1305
Polymers35,2611
Non-polymers8694
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)197.171, 279.324, 170.046
Angle α, β, γ (deg.)90.000, 125.091, 90.000
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

#1: Protein
Isoform 4 of Mesothelin / CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor


Mass: 35261.242 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q13421

-
Sugars , 3 types, 6 molecules

#2: 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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#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.: 4
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

-
Non-polymers , 2 types, 15 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 10
Source method: isolated from a genetically manipulated source
Formula: PO4
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3

-
Details

Has ligand of interestN
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 9.05 Å3/Da / Density % sol: 86.42 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: 0.9-1.1 M sodium/potassium phosphate, pH 8.2

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.89197 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 8, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89197 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.3176
pseudo-merohedral221/2H-1/2K+L, -3/2H-1/2K-L, -L20.3291
pseudo-merohedral331/2H+1/2K+L, 3/2H-1/2K+L, -L30.2979
pseudo-merohedral44H, -K, -H-L40.0554
ReflectionResolution: 3.6→50 Å / Num. obs: 78378 / % possible obs: 91.4 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.123 / Net I/σ(I): 4.87
Reflection shellResolution: 3.6→3.73 Å / Rmerge(I) obs: 0.48 / Num. unique obs: 6674 / % possible all: 78.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0350refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 7UED

7ued


Resolution: 3.609→49.292 Å / Cor.coef. Fo:Fc: 0.879 / Cor.coef. Fo:Fc free: 0.842 / WRfactor Rfree: 0.262 / WRfactor Rwork: 0.237 / SU B: 29.87 / SU ML: 0.234 / Average fsc free: 0.9647 / Average fsc work: 0.9714 / Cross valid method: FREE R-VALUE / ESU R: 0.158 / ESU R Free: 0.1
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3105 3948 5.062 %
Rwork0.2908 74040 -
all0.292 --
obs-77988 91.046 %
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: 128.434 Å2
Baniso -1Baniso -2Baniso -3
1--6.781 Å2-0 Å213.9 Å2
2--2.742 Å2-0 Å2
3---4.039 Å2
Refinement stepCycle: LAST / Resolution: 3.609→49.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11757 0 203 0 11960
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01212222
X-RAY DIFFRACTIONr_bond_other_d0.0010.01611377
X-RAY DIFFRACTIONr_angle_refined_deg0.7971.64616609
X-RAY DIFFRACTIONr_angle_other_deg0.2641.55726645
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.68751479
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.9161054
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.252102153
X-RAY DIFFRACTIONr_dihedral_angle_6_deg9.59510515
X-RAY DIFFRACTIONr_chiral_restr0.0380.21918
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0213396
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022194
X-RAY DIFFRACTIONr_nbd_refined0.1910.23101
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.211172
X-RAY DIFFRACTIONr_nbtor_refined0.170.26164
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0730.26280
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1450.2234
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1710.220
X-RAY DIFFRACTIONr_nbd_other0.1410.2120
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.0730.22
X-RAY DIFFRACTIONr_mcbond_it0.4573.9015934
X-RAY DIFFRACTIONr_mcbond_other0.4573.9015934
X-RAY DIFFRACTIONr_mcangle_it0.8435.8487407
X-RAY DIFFRACTIONr_mcangle_other0.8435.8487408
X-RAY DIFFRACTIONr_scbond_it0.2783.9346288
X-RAY DIFFRACTIONr_scbond_other0.2783.9346289
X-RAY DIFFRACTIONr_scangle_it0.5235.8959202
X-RAY DIFFRACTIONr_scangle_other0.5235.8959203
X-RAY DIFFRACTIONr_lrange_it1.9349.11614092
X-RAY DIFFRACTIONr_lrange_other1.9349.11614092
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
3.609-3.70.4722270.46142640.46161460.9740.9873.07190.439
3.7-3.7980.4422210.42646460.42760660.9710.97180.23410.397
3.798-3.9040.3762300.38746970.38757920.9710.97585.06560.352
3.904-4.0190.3463290.36645290.36456640.9770.97685.76980.327
4.019-4.1450.3242320.33547020.33555390.9780.97689.07740.294
4.145-4.2840.3512180.31946600.32153900.9730.97790.50090.275
4.284-4.4380.3332390.31644040.31750970.9740.97991.09280.265
4.438-4.610.3182810.30743210.30850160.9720.97691.74640.261
4.61-4.8030.3052380.28143120.28247990.9750.97994.81140.234
4.803-5.0230.3012370.27241710.27346110.9770.9895.59750.225
5.023-5.2770.2971770.28239750.28343340.9660.97495.80060.237
5.277-5.5720.3621720.26438610.26841780.9530.97596.52940.219
5.572-5.9240.2621750.28436210.28339410.9720.97296.32070.236
5.924-6.3530.2751780.29134210.2936900.9710.96697.53390.24
6.353-6.890.2772020.26531530.26634030.960.96498.58950.219
6.89-7.5920.1991630.20629450.20631590.9750.97298.38560.183
7.592-8.5630.2491460.21826530.2228270.9570.96499.00960.201
8.563-10.0370.193990.20323560.20224620.9720.98199.71570.196
10.037-12.6870.255930.23619390.23720360.9480.95399.80350.232
12.687-20.0020.371910.26214100.26815080.7880.85299.53580.28
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)
12.2444-1.41311.12541.9639-0.56580.9509-0.1074-0.17830.19660.06230.0011-0.2002-0.0032-0.00990.10630.79360.0238-0.24490.4604-0.03891.101536.515160.294187.3873
20.7164-0.1443-0.26843.3563-0.28990.36660.2463-0.15080.06290.2337-0.1335-0.03660.1358-0.2322-0.11280.7565-0.2791-0.32110.5136-0.12081.2139-6.80569.667657.1311
32.750.60950.84620.4676-0.28140.9493-0.22620.0245-0.0586-0.05110.1467-0.0708-0.212-0.23970.07950.90180.1381-0.42040.8465-0.06731.018480.182668.5496117.515
40.639-0.7266-0.08541.5426-0.10150.26370.4188-0.14290.0309-0.5938-0.06980.1958-0.2961-0.2317-0.3491.4460.2529-0.28520.94050.14931.351895.1239103.3966107.3873
52.5659-0.93941.23910.4722-0.46690.7409-0.0924-0.15460.30580.1532-0.19050.0870.05340.21580.28281.0272-0.2277-0.50881.02640.1031.309925.259847.803257.9759
60.84830.97150.82611.46671.24991.3926-0.32960.4845-0.430.27790.4183-0.39630.0316-0.0762-0.08871.5351-0.216-0.13610.9405-0.33332.153919.6768148.64955.2009
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