[English] 日本語
Yorodumi
- PDB-4f3f: Crystal Structure of Msln7-64 MORAb-009 FAB complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4f3f
TitleCrystal Structure of Msln7-64 MORAb-009 FAB complex
Components
  • MORAb-009 Fab heavy chain
  • MORAb-009 Fab light chain
  • Mesothelin
KeywordsIMMUNE SYSTEM / Antibody Fab / Recognize mesothelin / 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
Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 - #40 / Mesothelin / Stereocilin-related / Mesothelin / Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 / Immunoglobulins / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsXia, D. / Pastan, I. / Ma, J. / Tang, W.K. / Esser, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Recognition of mesothelin by the therapeutic antibody MORAb-009: structural and mechanistic insights.
Authors: Ma, J. / Tang, W.K. / Esser, L. / Pastan, I. / Xia, D.
History
DepositionMay 9, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 11, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Source and taxonomy
Revision 1.2Mar 26, 2014Group: Database references
Revision 2.0Dec 25, 2019Group: Database references / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / struct_conn / struct_ref_seq_dif
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id ..._entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 2.1Sep 13, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: MORAb-009 Fab light chain
B: MORAb-009 Fab heavy chain
C: Mesothelin


Theoretical massNumber of molelcules
Total (without water)55,7193
Polymers55,7193
Non-polymers00
Water2,198122
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5260 Å2
ΔGint-31 kcal/mol
Surface area21510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.163, 146.163, 80.874
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number172
Space group name H-MP64

-
Components

#1: Antibody MORAb-009 Fab light chain


Mass: 23243.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#2: Antibody MORAb-009 Fab heavy chain


Mass: 24422.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
#3: Protein Mesothelin / CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor / Megakaryocyte-potentiating factor / MPF ...CAK1 antigen / Pre-pro-megakaryocyte-potentiating factor / Megakaryocyte-potentiating factor / MPF / Mesothelin / cleaved form


Mass: 8053.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: MSLN, MPF / Production host: Escherichia coli (E. coli) / References: UniProt: Q13421
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.48 Å3/Da / Density % sol: 72.52 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.1 M Trisodium citrate pH 5.6, 17% Polyethylene glycol 3350, VAPOR DIFFUSION, HANGING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 8, 2011 / Details: Mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.61→50 Å / Num. all: 29927 / Num. obs: 29264 / % possible obs: 97.8 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 2.61→2.7 Å / Redundancy: 2.4 % / Mean I/σ(I) obs: 1.76 / Num. unique all: 2373 / Rsym value: 0.101 / % possible all: 80

-
Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: dev_965)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4F33, Difference Fourier revealed MSLN7-64

4f33


Resolution: 2.65→34.076 Å / SU ML: 0.38 / σ(F): 0.66 / Phase error: 22.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.222 1448 5.1 %Random
Rwork0.1771 ---
all0.1794 28414 --
obs0.1794 28414 98.89 %-
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.3 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 21.96 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-25.2257 Å20 Å2-0 Å2
2--25.2257 Å20 Å2
3----1.1986 Å2
Refinement stepCycle: LAST / Resolution: 2.65→34.076 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3727 0 0 122 3849
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173820
X-RAY DIFFRACTIONf_angle_d1.5845178
X-RAY DIFFRACTIONf_dihedral_angle_d17.6231383
X-RAY DIFFRACTIONf_chiral_restr0.076578
X-RAY DIFFRACTIONf_plane_restr0.007657
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.65-2.74470.33131190.30132449X-RAY DIFFRACTION90
2.7447-2.85450.33261360.25882681X-RAY DIFFRACTION99
2.8545-2.98440.27551440.23612739X-RAY DIFFRACTION100
2.9844-3.14160.26731490.21072672X-RAY DIFFRACTION100
3.1416-3.33830.25841510.20422731X-RAY DIFFRACTION100
3.3383-3.59580.22191390.18712694X-RAY DIFFRACTION100
3.5958-3.95720.22711640.16942728X-RAY DIFFRACTION100
3.9572-4.52860.1961510.14052721X-RAY DIFFRACTION100
4.5286-5.70130.18461450.14132745X-RAY DIFFRACTION100
5.7013-34.07860.18741500.16282806X-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)
12.3904-1.29710.92434.4417-0.55554.43780.0243-0.1407-0.3123-0.09560.2017-0.08610.47020.1431-0.1690.1992-0.0247-0.03780.2364-0.02890.250773.77220.9665.196
21.63040.2965-0.04532.3481-0.79821.6159-0.2290.1051-0.287-0.39580.57350.9580.0333-0.72310.04170.3752-0.1544-0.08220.4580.14690.74751.3466-7.0561.8226
31.3974-0.3554-0.69651.89-0.30185.27110.2207-0.0416-0.2063-0.20840.17360.53540.5302-1.37-0.30260.2832-0.0896-0.08040.56380.24520.420551.018527.5978-9.3711
42.4686-0.54490.60445.00020.73112.80420.0848-0.0674-0.2186-0.3650.19740.2465-0.0596-0.1389-0.25270.1831-0.0597-0.0080.28220.04910.213862.375633.2353-8.5619
51.98591.07511.07652.5314-0.0272.70770.07220.108-0.1004-0.36120.37710.16960.1842-0.1954-0.39610.2499-0.0537-0.03420.3060.08120.257260.438429.5347-6.7116
61.30811.6419-0.072.207-0.02420.0552-0.1158-0.1569-0.4195-0.50220.52910.73640.3044-0.50130.03450.4063-0.1915-0.2360.70980.29030.808445.627113.2375-9.9665
73.52310.33760.44533.47390.79276.9407-0.3138-0.4736-0.02260.24370.63441.2892-0.4016-1.1555-0.29440.51620.1097-0.01120.6740.28720.936742.24635.47853.5503
85.2187-2.41295.64287.2116-5.61768.38550.30971.1915-0.3771-1.1065-0.1593-0.45780.7392.0508-0.01490.44490.00680.06310.5442-0.05690.338486.240640.8932-6.5999
94.9443-1.0787-0.05074.8376-0.98217.1455-0.2190.2672-0.3294-0.7270.31480.11530.90710.2142-0.19040.3067-0.10910.02660.2509-0.00960.194576.05938.5316-6.9756
103.6808-0.04941.48060.32420.97323.75740.02110.01610.948-0.1621-0.14540.1429-0.58780.48420.22920.3201-0.1526-0.04130.35290.02310.319578.216747.476-7.3569
116.73751.8941-1.79786.4256-1.16194.49320.3142-0.96011.09021.132-0.1685-0.0089-0.87370.14-0.07580.55640.0236-0.02930.2461-0.06170.338874.996151.7166-1.0931
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 101 )
2X-RAY DIFFRACTION2chain 'A' and (resid 102 through 212 )
3X-RAY DIFFRACTION3chain 'B' and (resid 2 through 25 )
4X-RAY DIFFRACTION4chain 'B' and (resid 26 through 76 )
5X-RAY DIFFRACTION5chain 'B' and (resid 77 through 109 )
6X-RAY DIFFRACTION6chain 'B' and (resid 110 through 130 )
7X-RAY DIFFRACTION7chain 'B' and (resid 131 through 220 )
8X-RAY DIFFRACTION8chain 'C' and (resid 6 through 17 )
9X-RAY DIFFRACTION9chain 'C' and (resid 18 through 24 )
10X-RAY DIFFRACTION10chain 'C' and (resid 25 through 50 )
11X-RAY DIFFRACTION11chain 'C' and (resid 51 through 64 )

+
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://pdbjlvh1.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