[English] 日本語
Yorodumi
- PDB-7u8c: Crystal structure of Mesothelin C-terminal peptide-MORAb 15B6 FAB... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7u8c
TitleCrystal structure of Mesothelin C-terminal peptide-MORAb 15B6 FAB complex
Components
  • MORab 15B6 Fab heavy chain
  • MORab 15B6 Fab light chain
  • Mesothelin, cleaved form
KeywordsIMMUNE SYSTEM / 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 / cell surface / Golgi apparatus / 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 / cell surface / Golgi apparatus / extracellular region / membrane / plasma membrane
Similarity search - Function
Mesothelin / Stereocilin-related / Mesothelin
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.74 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: Proc.Natl.Acad.Sci.USA / Year: 2022
Title: Highly active CAR T cells that bind to a juxtamembrane region of mesothelin and are not blocked by shed mesothelin.
Authors: Liu, X. / Onda, M. / Watson, N. / Hassan, R. / Ho, M. / Bera, T.K. / Wei, J. / Chakraborty, A. / Beers, R. / Zhou, Q. / Shajahan, A. / Azadi, P. / Zhan, J. / Xia, D. / Pastan, I.
History
DepositionMar 8, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
BA2: Mesothelin, cleaved form
H: MORab 15B6 Fab heavy chain
L: MORab 15B6 Fab light chain


Theoretical massNumber of molelcules
Total (without water)47,5273
Polymers47,5273
Non-polymers00
Water5,603311
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4790 Å2
ΔGint-33 kcal/mol
Surface area20240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.832, 64.832, 250.134
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11H-301-

HOH

21H-431-

HOH

-
Components

#1: Protein/peptide Mesothelin, cleaved form


Mass: 1863.138 Da / Num. of mol.: 1 / Fragment: C-terminal peptide (UNP residues 590-606) / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q13421
#2: Antibody MORab 15B6 Fab heavy chain


Mass: 22799.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#3: Antibody MORab 15B6 Fab light chain


Mass: 22864.312 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Mus musculus (house mouse)
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 311 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.77 Å3/Da / Density % sol: 55.61 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate, pH 4.5, 26% PEG550 MME, 6% 2-propanol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.03317 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03317 Å / Relative weight: 1
ReflectionResolution: 1.74→50 Å / Num. obs: 53658 / % possible obs: 95.3 % / Redundancy: 27.4 % / Biso Wilson estimate: 30.07 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.092 / Net I/σ(I): 35
Reflection shellResolution: 1.74→1.8 Å / Rmerge(I) obs: 0.497 / Num. unique obs: 3899

-
Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DENZOdata reduction
SCALEPACKdata scaling
BALBESphasing
HKL-2000data collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3RIF

3rif


Resolution: 1.74→24.01 Å / SU ML: 0.2218 / Cross valid method: FREE R-VALUE / σ(F): 1.01 / Phase error: 26.3108
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2383 2770 5.17 %
Rwork0.2043 50761 -
obs0.2061 53531 95.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.17 Å2
Refinement stepCycle: LAST / Resolution: 1.74→24.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3322 0 0 311 3633
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00293405
X-RAY DIFFRACTIONf_angle_d0.53434651
X-RAY DIFFRACTIONf_chiral_restr0.0442539
X-RAY DIFFRACTIONf_plane_restr0.0031586
X-RAY DIFFRACTIONf_dihedral_angle_d11.83651189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.74-1.770.3716880.36911661X-RAY DIFFRACTION63.37
1.77-1.80.37231320.3491995X-RAY DIFFRACTION76.9
1.8-1.840.3841160.34592188X-RAY DIFFRACTION83.97
1.84-1.870.32681250.33932282X-RAY DIFFRACTION88.59
1.87-1.910.33371530.31672483X-RAY DIFFRACTION94.11
1.91-1.960.35421250.30672615X-RAY DIFFRACTION99.6
1.96-2.010.30161510.29472578X-RAY DIFFRACTION99.89
2.01-2.060.32151340.26882617X-RAY DIFFRACTION99.89
2.06-2.120.29111480.25582630X-RAY DIFFRACTION99.96
2.12-2.190.30241400.23252653X-RAY DIFFRACTION99.79
2.19-2.270.26381520.21252609X-RAY DIFFRACTION99.93
2.27-2.360.24641500.2092627X-RAY DIFFRACTION99.96
2.36-2.470.24951440.20382659X-RAY DIFFRACTION99.86
2.47-2.60.23111490.1942658X-RAY DIFFRACTION99.86
2.6-2.760.23881480.20142651X-RAY DIFFRACTION99.96
2.76-2.970.23881420.21742697X-RAY DIFFRACTION99.96
2.97-3.270.22091190.20662723X-RAY DIFFRACTION99.93
3.27-3.740.23721270.19132725X-RAY DIFFRACTION100
3.74-4.710.19281620.15342768X-RAY DIFFRACTION100
4.71-24.010.20751650.17792942X-RAY DIFFRACTION99.84
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)
12.23364589296-0.852472134457-2.783374497484.375068073092.713752414247.01797819961-0.460952823265-0.4796005827590.1850692517651.323961786350.212365189401-0.2653479123450.4160204924080.673688924870.2040872551950.5246060693190.101873907919-0.03997462836320.8285711910650.06539627370620.31238712480912.1635830533-8.7891071713258.3586865499
25.17055258045-4.6098381572-1.313264395985.937092882291.60215884174.39679953566-0.662256042233-0.504959720310.1486607196331.131562954410.27041496397-0.5356630543140.2387625669330.779152913180.191628250610.3359193245420.0859930760663-0.01760323556580.973163770930.02184332435630.33587957991920.8723997214-18.106300814151.0457557672
31.274297816930.1939879240.6746320439691.55449913119-0.3184438183133.96051711686-0.13780040459-0.1540237641950.132880341041-0.04621571869770.08571127144660.0397907940222-0.5884741139080.2242778004680.07473941865980.210166261507-0.0384830782142-0.0538028418730.5885045047660.06735926340590.36529287685811.3413495293-0.81283907767137.4232006991
41.828783686190.9708537719570.7351744217197.58300754993-0.2388242921053.499541052260.03932952104710.79550379998-0.100415347035-1.676939555350.203401804075-1.19334466509-0.1481693145271.05892630399-0.2421316363040.814287563533-0.116853692299-0.0133144938990.9784413758730.1091410250720.59611622750715.4768364287-11.2929414217-6.22473367896
51.45362578142-0.4772706076530.2324157750352.282068135750.9049956975154.49106295739-0.1594641601790.246397881049-0.209080312846-0.4579729635260.0455110111360.202038129269-0.1316844440210.09351536612570.03401044108370.499362653033-0.165838518452-0.1363642838470.6669076058390.2217968268010.4190626922337.27311805654-8.472299653163.09300762759
61.78391899743-0.4111281875160.07355530376980.7335402071620.0784007241740.54149467679-0.0242626142413-0.1879638777910.1173046281010.06316392378080.0422561137153-0.3859112725630.04962857022330.252760897726-0.1162761988810.142517263467-0.0156574899874-4.45411489417E-50.8429095837680.08903726215840.42758999042529.1195867737-20.271529451833.3180617899
71.3011466257-0.1143478744470.3326820761160.9835255052310.2941288577061.11940372163-0.199499777396-0.383341768579-0.08243045877420.1231470460750.149664633694-0.07708799378990.2270886839890.208606654674-0.1343833864860.1134323719910.0177166248656-0.01892100195240.8184814321290.1208361631030.38776055259420.5466598176-19.250756087637.8987554388
80.762460520618-0.3579358858620.6820745589980.4627334097720.5720435303883.29399981067-0.06047243567690.1582398573860.0773331154402-0.1524497969440.03403188009880.0239180273549-0.04545533858320.317573132732-0.01847809532730.219575635854-0.05117100652010.03296770158150.6694567297570.0993210140350.38297244594420.1788294256-26.93717796318.5132129646
91.21152320495-0.5993344137740.1701137086034.86341487523-0.9961956550181.1795150586-0.01319640437790.5039835237060.273621857729-0.720620752918-0.129972099961-0.0985500503414-0.4433760111950.5150573717290.1732615007110.547194718959-0.199572763409-0.07523729876920.9030426132570.2760806785430.41855042694918.9076306184-7.086115038870.52694806392
101.31827793352-0.196232810541-0.230761165112.447663955960.01801127833570.571871243272-0.09724851099450.3852146896190.209666035365-0.293577930339-0.000708272220104-0.306446546379-0.416645154530.4421470016190.05504173274470.445079660988-0.241552259411-0.05299617867310.8892891904770.2453085578190.4619800660323.8758979583-9.968754183738.14591072245
110.390016008401-0.3585506697450.07903286112221.251002709490.4969208301620.7252682972570.1128067944260.2613338387230.222517855182-0.890700793023-0.0682736106865-0.280897959381-0.2053073183160.3560756073930.09569929016960.582628738079-0.123877426950.0722204077481.082818732260.2007643899010.48605137144929.2945328791-13.98893502860.856009443735
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'BA2' and (resid 584 through 590 )BA2A584 - 5901 - 7
22chain 'BA2' and (resid 591 through 598 )BA2A591 - 5988 - 15
33chain 'H' and (resid 1 through 120 )HB1 - 1201 - 120
44chain 'H' and (resid 121 through 135 )HB121 - 135121 - 135
55chain 'H' and (resid 136 through 214 )HB136 - 214136 - 214
66chain 'L' and (resid 1 through 30 )LC1 - 301 - 30
77chain 'L' and (resid 31 through 103 )LC31 - 10331 - 103
88chain 'L' and (resid 104 through 116 )LC104 - 116104 - 116
99chain 'L' and (resid 117 through 142 )LC117 - 142117 - 142
1010chain 'L' and (resid 143 through 190 )LC143 - 190143 - 190
1111chain 'L' and (resid 191 through 213 )LC191 - 213191 - 213

+
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