[English] 日本語
Yorodumi
- PDB-4mzv: Crystal structure of extracellular part of human EpCAM -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4mzv
TitleCrystal structure of extracellular part of human EpCAM
ComponentsEpithelial cell adhesion molecule
KeywordsCELL ADHESION / ECTODOMAIN / DIMER / EXTRACELLULAR SPACE
Function / homology
Function and homology information


cadherin binding involved in cell-cell adhesion / negative regulation of cell-cell adhesion mediated by cadherin / signal transduction involved in regulation of gene expression / ureteric bud development / positive regulation of stem cell proliferation / lateral plasma membrane / bicellular tight junction / stem cell differentiation / Cell surface interactions at the vascular wall / basolateral plasma membrane ...cadherin binding involved in cell-cell adhesion / negative regulation of cell-cell adhesion mediated by cadherin / signal transduction involved in regulation of gene expression / ureteric bud development / positive regulation of stem cell proliferation / lateral plasma membrane / bicellular tight junction / stem cell differentiation / Cell surface interactions at the vascular wall / basolateral plasma membrane / apical plasma membrane / positive regulation of cell population proliferation / protein-containing complex binding / cell surface / positive regulation of transcription by RNA polymerase II / extracellular exosome / plasma membrane
Similarity search - Function
Epithelial cell adhesion molecule N-terminal domain / Transmembrane glycoprotein EPCAM/Trop-2 / : / Epithelial cell adhesion molecule, N-terminal domain / EPCAM/Trop-2, C-terminal / Thyroglobulin type-1 repeat signature. / Thyroglobulin type-1 / Thyroglobulin type-1 superfamily / Thyroglobulin type-1 repeat / Thyroglobulin type-1 domain profile. / Thyroglobulin type I repeats.
Similarity search - Domain/homology
Epithelial cell adhesion molecule
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SAD / Resolution: 1.865 Å
AuthorsPavsic, M. / Guncar, G. / Djinovic-Carugo, K. / Lenarcic, B.
CitationJournal: Nat Commun / Year: 2014
Title: Crystal structure and its bearing towards an understanding of key biological functions of EpCAM.
Authors: Pavsic, M. / Guncar, G. / Djinovic-Carugo, K. / Lenarcic, B.
History
DepositionSep 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Sep 10, 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 / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Epithelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7602
Polymers28,2771
Non-polymers4831
Water2,648147
1
A: Epithelial cell adhesion molecule
hetero molecules

A: Epithelial cell adhesion molecule
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,5194
Polymers56,5542
Non-polymers9652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7010 Å2
ΔGint-20 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.022, 50.385, 67.828
Angle α, β, γ (deg.)90.00, 128.33, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-488-

HOH

-
Components

#1: Protein Epithelial cell adhesion molecule / Ep-CAM / Adenocarcinoma-associated antigen / Cell surface glycoprotein Trop-1 / Epithelial cell ...Ep-CAM / Adenocarcinoma-associated antigen / Cell surface glycoprotein Trop-1 / Epithelial cell surface antigen / Epithelial glycoprotein / EGP / Epithelial glycoprotein 314 / EGP314 / hEGP314 / KS 1/4 antigen / KSA / Major gastrointestinal tumor-associated protein GA733-2 / Tumor-associated calcium signal transducer 1


Mass: 28276.984 Da / Num. of mol.: 1 / Fragment: UNP residues 24-265 / Mutation: N74Q, N111Q, N198Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: EPCAM, GA733-2, M1S2, M4S1, MIC18, TACSTD1, TROP1 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Sf9 / References: UniProt: P16422
#2: Sugar ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THE PYROGLUTAMATE RESIDUE IS A POST-TRANSLATIONALLY MODIFIED N-TERMINAL GLN ...AUTHORS STATE THAT THE PYROGLUTAMATE RESIDUE IS A POST-TRANSLATIONALLY MODIFIED N-TERMINAL GLN RESIDUE AFTER SIGNAL PEPTIDE CLEAVAGE. THE THR OR MET AT POSITION 115 ARE TWO NATURAL VARIANTS ACCORDING TO UNIPROT SEQUENCE DATABASE.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.2M magnesium chloride, 0.1M TRIS-HCl, 30% w/v PEG 4000, 0.16 mM decyl-beta-D-maltopyranoside, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.542 Å
DetectorType: Bruker Platinum 135 / Detector: CCD / Date: Feb 2, 2010
RadiationMonochromator: MULTILAYER X-RAY MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 1.86→27.794 Å / Num. obs: 18527 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 26.6 % / Biso Wilson estimate: 29.74 Å2 / Net I/σ(I): 33.98
Reflection shell
Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique allDiffraction-ID% possible all
1.86-1.916.332.61788185.5
1.91-1.959.193.6121911100
1.95-1.9910.274.4619811100
1.99-2.0311.416.1919011100
2.03-2.0812.817.7420911100
2.08-2.13148.819411100
2.13-2.1915.6611.6920861100
2.19-2.2618.0714.5921541100
2.26-2.3421.0918.9621451100
2.34-2.4225.3824.619041100
2.42-2.5231.3330.2520031100
2.52-2.6436.4437.9620551100
2.64-2.7838.6146.0219401100
2.78-2.9639.8452.3120321100
2.96-3.1941.6362.8219411100
3.19-3.5142.5671.9219091100
3.51-4.0244.2678.1219381100
4.02-5.0647.0486.4119231100
5.06-27.7946.1986.541905199.6

-
Processing

Software
NameVersionClassification
PROTEUM2data collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
PROTEUM2data reduction
PROTEUM2data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.865→27.79 Å / SU ML: 0.21 / σ(F): 1.33 / Phase error: 29.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2491 949 5.12 %RANDOM
Rwork0.1935 ---
obs0.1965 18527 94.56 %-
all-19594 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.865→27.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1924 0 33 147 2104
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011993
X-RAY DIFFRACTIONf_angle_d1.2732679
X-RAY DIFFRACTIONf_dihedral_angle_d15.339755
X-RAY DIFFRACTIONf_chiral_restr0.084305
X-RAY DIFFRACTIONf_plane_restr0.005343
LS refinement shell

Refine-ID: X-RAY DIFFRACTION

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection obs% reflection obs (%)
1.865-1.9630.29971180.25742460257792
1.963-2.08590.34951200.25162414253492
2.0859-2.24690.30641350.23212439257492
2.2469-2.47290.32271180.22882466258493
2.4729-2.83040.2951570.22962540269796
2.8304-3.56490.25351340.18762576271097
3.5649-27.79740.19771670.15792684285199
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)
10.5072-1.80682.28272.414-3.43553.8380.05390.06530.12280.1286-0.151-0.166-0.33070.27450.11850.2953-0.0295-0.03950.34570.06740.2714.022942.273912.17
23.3121-0.0585-0.17772.6259-0.90732.73840.1095-0.30210.03640.3717-0.14370.0113-0.12480.19630.00020.20680.00410.02150.18120.0020.1184-2.232450.192313.9662
34.1726-0.65510.06453.95150.27982.83030.0662-0.2511-0.20310.22780.0864-0.0280.03320.1744-0.08990.1903-0.0489-0.01550.23610.02190.1441-4.567845.662512.8701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND (RESID 24:92)
2X-RAY DIFFRACTION2CHAIN A AND (RESID 93:187)
3X-RAY DIFFRACTION3CHAIN A AND (RESID 188:266)

+
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