[English] 日本語
Yorodumi
- PDB-8vrs: Mucin 16 peptide fused to MBP in complex with 4H11-scFv antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8vrs
TitleMucin 16 peptide fused to MBP in complex with 4H11-scFv antibody
Components
  • 4H11 scFv chain
  • Maltose/maltodextrin-binding periplasmic protein,Mucin-16
KeywordsONCOPROTEIN/IMMUNE SYSTEM / ANTIBODY COMPLEX EPITOPE CANCER THERAPY IMMUNOTHERAPY MUCINS / ONCOPROTEIN / ONCOPROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / detection of maltose stimulus / maltose transport complex / Dectin-2 family / maltose binding / maltose transport ...Defective GALNT3 causes HFTC / Defective C1GALT1C1 causes TNPS / Defective GALNT12 causes CRCS1 / Termination of O-glycan biosynthesis / O-linked glycosylation of mucins / detection of maltose stimulus / maltose transport complex / Dectin-2 family / maltose binding / maltose transport / maltodextrin transmembrane transport / carbohydrate transport / carbohydrate transmembrane transporter activity / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / Golgi lumen / outer membrane-bounded periplasmic space / vesicle / periplasmic space / cell adhesion / external side of plasma membrane / DNA damage response / extracellular exosome / membrane / plasma membrane
Similarity search - Function
Mucin-16 / Domain found in sea urchin sperm protein, enterokinase, agrin / SEA domain superfamily / SEA domain profile. / SEA domain / SEA domain / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Mucin-16
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Homo sapiens (human)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsLee, K. / Perry, K. / Yeku, O.O. / Spriggs, D.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI)1P01 CA190174-01A1 United States
CitationJournal: J Ovarian Res / Year: 2024
Title: Structural basis for antibody recognition of the proximal MUC16 ectodomain.
Authors: Lee, K. / Perry, K. / Xu, M. / Veillard, I. / Kumar, R. / Rao, T.D. / Rueda, B.R. / Spriggs, D.R. / Yeku, O.O.
History
DepositionJan 22, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Maltose/maltodextrin-binding periplasmic protein,Mucin-16
C: 4H11 scFv chain
B: Maltose/maltodextrin-binding periplasmic protein,Mucin-16
D: 4H11 scFv chain


Theoretical massNumber of molelcules
Total (without water)142,2274
Polymers142,2274
Non-polymers00
Water6,341352
1
A: Maltose/maltodextrin-binding periplasmic protein,Mucin-16
D: 4H11 scFv chain


Theoretical massNumber of molelcules
Total (without water)71,1132
Polymers71,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2290 Å2
ΔGint-9 kcal/mol
Surface area25760 Å2
MethodPISA
2
C: 4H11 scFv chain
B: Maltose/maltodextrin-binding periplasmic protein,Mucin-16


Theoretical massNumber of molelcules
Total (without water)71,1132
Polymers71,1132
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-7 kcal/mol
Surface area25570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.810, 112.634, 110.808
Angle α, β, γ (deg.)90.000, 101.253, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

-
Components

#1: Protein Maltose/maltodextrin-binding periplasmic protein,Mucin-16 / MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / MUC-16 / Ovarian cancer- ...MMBP / Maltodextrin-binding protein / Maltose-binding protein / MBP / MUC-16 / Ovarian cancer-related tumor marker CA125 / CA-125 / Ovarian carcinoma antigen CA125


Mass: 43664.215 Da / Num. of mol.: 2 / Fragment: residues 14421-14446 of mucin-16
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli), (gene. exp.) Homo sapiens (human)
Gene: malE, b4034, JW3994, MUC16, CA125 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL (DE3) / References: UniProt: P0AEX9, UniProt: Q8WXI7
#2: Antibody 4H11 scFv chain


Mass: 27449.221 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): HEK293T/17 / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 352 / 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: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1M Sodium Citrate, pH 5.0, 10mM Barium Chloride, 27% PEG MME 5000

-
Data collection

DiffractionMean temperature: 183 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 5, 2020 / Details: KB Mirrors
RadiationMonochromator: Single Crystal Si-220 Side Bounce / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.47→112.63 Å / Num. obs: 51394 / % possible obs: 98.9 % / Redundancy: 3.5 % / Biso Wilson estimate: 42.06 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.083 / Rpim(I) all: 0.079 / Rrim(I) all: 0.115 / Net I/σ(I): 9.2
Reflection shellResolution: 2.47→2.54 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 4270 / CC1/2: 0.683 / Rpim(I) all: 0.617 / Rrim(I) all: 0.91 / % possible all: 95.2

-
Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.47→56.43 Å / SU ML: 0.3297 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 27.6006
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2369 1836 3.87 %
Rwork0.1918 45655 -
obs0.1936 47491 91.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 49.04 Å2
Refinement stepCycle: LAST / Resolution: 2.47→56.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9688 0 0 352 10040
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00979910
X-RAY DIFFRACTIONf_angle_d1.385413434
X-RAY DIFFRACTIONf_chiral_restr0.05581450
X-RAY DIFFRACTIONf_plane_restr0.00611740
X-RAY DIFFRACTIONf_dihedral_angle_d20.29733596
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.47-2.530.34461160.29312867X-RAY DIFFRACTION75.08
2.53-2.610.31481260.28253151X-RAY DIFFRACTION81.44
2.61-2.690.32171270.25793180X-RAY DIFFRACTION83.89
2.69-2.790.29541380.25333353X-RAY DIFFRACTION87.82
2.79-2.90.32761330.24293417X-RAY DIFFRACTION88.88
2.9-3.030.28571430.23363498X-RAY DIFFRACTION91.07
3.03-3.190.26211510.22673544X-RAY DIFFRACTION92.77
3.19-3.390.24421340.21013686X-RAY DIFFRACTION95.98
3.39-3.650.25551570.18213727X-RAY DIFFRACTION97
3.65-4.020.22091570.17543788X-RAY DIFFRACTION98.23
4.02-4.60.1871530.14673765X-RAY DIFFRACTION97.56
4.6-5.80.19851470.15113802X-RAY DIFFRACTION98.77
5.8-56.430.20151540.1823877X-RAY DIFFRACTION98.56
Refinement TLS params.Method: refined / Origin x: 1.25935758897 Å / Origin y: -15.7451563189 Å / Origin z: 28.5610980628 Å
111213212223313233
T0.340201031489 Å2-0.00146453647952 Å2-0.000643585498194 Å2-0.340069684053 Å2-0.0133402389829 Å2--0.359298903466 Å2
L0.0399273412292 °20.0125172162595 °2-0.0132194569798 °2-0.00387384496443 °20.00124575780238 °2--0.0276315498491 °2
S-0.00330864861887 Å °0.00872357962368 Å °-0.00313821379015 Å °0.0154755152647 Å °0.00234858668879 Å °-0.0290568090245 Å °0.00472004808482 Å °-0.0277833361462 Å °-1.18337355992E-5 Å °
Refinement TLS groupSelection details: 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