[English] 日本語
Yorodumi
- PDB-8ghp: GUCY2C-ECD bound to anti-GUCY2C-scFv antibody -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8ghp
TitleGUCY2C-ECD bound to anti-GUCY2C-scFv antibody
Components
  • Guanylyl cyclase C
  • anti-GUCY2C-scFv antibody heavy chain
  • anti-GUCY2C-scFv antibody light chain
KeywordsPROTEIN BINDING / bi-specific antibody GUCY2C antigen
Function / homology
Function and homology information


Intestinal infectious diseases / Digestion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / adenylate cyclase activity / toxic substance binding / response to toxic substance ...Intestinal infectious diseases / Digestion / receptor guanylyl cyclase signaling pathway / peptide receptor activity / guanylate cyclase / guanylate cyclase activity / cGMP biosynthetic process / adenylate cyclase activity / toxic substance binding / response to toxic substance / regulation of cell population proliferation / protein kinase activity / intracellular signal transduction / GTP binding / endoplasmic reticulum membrane / ATP binding / plasma membrane
Similarity search - Function
Membrane Guanylate Cyclase receptor GC-C, pseudokinase domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Periplasmic binding protein-like I / Protein tyrosine and serine/threonine kinase ...Membrane Guanylate Cyclase receptor GC-C, pseudokinase domain / Adenylyl cyclase class-4/guanylyl cyclase, conserved site / Guanylate cyclase signature. / Adenylyl- / guanylyl cyclase, catalytic domain / Adenylyl cyclase class-3/4/guanylyl cyclase / Adenylate and Guanylate cyclase catalytic domain / Guanylate cyclase domain profile. / Nucleotide cyclase / Periplasmic binding protein-like I / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.52 Å
AuthorsMosyak, L.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2023
Title: Molecular insights into recognition of GUCY2C by T-cell engaging bispecific antibody anti-GUCY2CxCD3.
Authors: Rampuria, P. / Mosyak, L. / Root, A.R. / Svenson, K. / Agostino, M.J. / LaVallie, E.R.
History
DepositionMar 10, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 30, 2023Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Guanylyl cyclase C
H: anti-GUCY2C-scFv antibody heavy chain
L: anti-GUCY2C-scFv antibody light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6594
Polymers74,0313
Non-polymers6281
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)199.629, 199.629, 123.267
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein Guanylyl cyclase C / GC-C / Heat-stable enterotoxin receptor / STA receptor / hSTAR / Intestinal guanylate cyclase


Mass: 47410.453 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUCY2C, GUC2C, STAR / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P25092, guanylate cyclase
#2: Antibody anti-GUCY2C-scFv antibody heavy chain


Mass: 13637.258 Da / Num. of mol.: 1 / Fragment: VH domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody anti-GUCY2C-scFv antibody light chain


Mass: 12983.392 Da / Num. of mol.: 1 / Fragment: VL domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.39 Å3/Da / Density % sol: 80.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 2M ammonium H2-PO4, 100mM Tris hydrochloride at pH 8.5

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.52→60 Å / Num. obs: 17636 / % possible obs: 91.8 % / Redundancy: 5.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.3
Reflection shellResolution: 3.52→3.77 Å / Rmerge(I) obs: 0.9 / Num. unique obs: 881

-
Processing

Software
NameClassification
BUSTERrefinement
autoPROCdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.52→34.21 Å / Cor.coef. Fo:Fc: 0.785 / Cor.coef. Fo:Fc free: 0.782 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.549
RfactorNum. reflection% reflectionSelection details
Rfree0.282 763 4.33 %RANDOM
Rwork0.274 ---
obs0.275 17612 77.8 %-
Displacement parametersBiso mean: 105.43 Å2
Baniso -1Baniso -2Baniso -3
1-2.0668 Å20 Å20 Å2
2--2.0668 Å20 Å2
3----4.1337 Å2
Refine analyzeLuzzati coordinate error obs: 0.88 Å
Refinement stepCycle: 1 / Resolution: 3.52→34.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5060 0 42 0 5102
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0085228HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.17097HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1789SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes876HARMONIC5
X-RAY DIFFRACTIONt_it5228HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.53
X-RAY DIFFRACTIONt_other_torsion17.54
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion684SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact5695SEMIHARMONIC4
LS refinement shellResolution: 3.52→3.74 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2269 -5.34 %
Rwork0.2211 620 -
all0.2214 655 -
obs--17.84 %

+
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