[English] 日本語
Yorodumi
- PDB-7rpp: Crystal structure of human CEACAM1 with GFCC' and ABED face -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7rpp
TitleCrystal structure of human CEACAM1 with GFCC' and ABED face
ComponentsCarcinoembryonic antigen-related cell adhesion molecule 1
KeywordsIMMUNE SYSTEM / CEACAM1
Function / homology
Function and homology information


regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / filamin binding ...regulation of endothelial cell differentiation / insulin receptor internalization / negative regulation of cytotoxic T cell degranulation / granulocyte colony-stimulating factor signaling pathway / regulation of homophilic cell adhesion / regulation of sprouting angiogenesis / regulation of epidermal growth factor receptor signaling pathway / regulation of blood vessel remodeling / negative regulation of hepatocyte proliferation / filamin binding / negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target / negative regulation of lipid biosynthetic process / bile acid transmembrane transporter activity / negative regulation of T cell mediated cytotoxicity / regulation of endothelial cell migration / negative regulation of granulocyte differentiation / Fibronectin matrix formation / insulin catabolic process / common myeloid progenitor cell proliferation / negative regulation of interleukin-1 production / negative regulation of fatty acid biosynthetic process / positive regulation of vasculogenesis / cell-cell adhesion via plasma-membrane adhesion molecules / negative regulation of platelet aggregation / regulation of immune system process / bile acid and bile salt transport / negative regulation of vascular permeability / wound healing, spreading of cells / transport vesicle membrane / microvillus membrane / negative regulation of T cell receptor signaling pathway / blood vessel development / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / homophilic cell adhesion via plasma membrane adhesion molecules / tertiary granule membrane / lateral plasma membrane / specific granule membrane / regulation of cell migration / regulation of ERK1 and ERK2 cascade / protein tyrosine kinase binding / basal plasma membrane / integrin-mediated signaling pathway / regulation of cell growth / Cell surface interactions at the vascular wall / adherens junction / negative regulation of protein kinase activity / kinase binding / cellular response to insulin stimulus / cell-cell junction / cell migration / cell junction / actin binding / protein phosphatase binding / angiogenesis / protein dimerization activity / calmodulin binding / cell adhesion / apical plasma membrane / Neutrophil degranulation / cell surface / signal transduction / protein homodimerization activity / extracellular exosome / identical protein binding / membrane / plasma membrane
Similarity search - Function
Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin ...Immunoglobulin domain / Immunoglobulin / Immunoglobulin domain / Immunoglobulin domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Carcinoembryonic antigen-related cell adhesion molecule 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsGandhi, A.K. / Kim, W.M. / Sun, Z.-Y. / Huang, Y.H. / Petsko, G.A. / Blumberg, R.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Library of Medicine (NIH/NLM) United States
CitationJournal: Commun Biol / Year: 2022
Title: Structural analysis of human CEACAM1 oligomerization.
Authors: Gandhi, A.K. / Sun, Z.J. / Huang, Y.H. / Kim, W.M. / Yang, C. / Petsko, G.A. / Beauchemin, N. / Blumberg, R.S.
History
DepositionAug 4, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 10, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Carcinoembryonic antigen-related cell adhesion molecule 1
B: Carcinoembryonic antigen-related cell adhesion molecule 1
C: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8225
Polymers35,6983
Non-polymers1242
Water1,33374
1
A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules

A: Carcinoembryonic antigen-related cell adhesion molecule 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,0476
Polymers23,7982
Non-polymers2484
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,y,-z1
Buried area2350 Å2
ΔGint-2 kcal/mol
Surface area10320 Å2
MethodPISA
2
B: Carcinoembryonic antigen-related cell adhesion molecule 1
C: Carcinoembryonic antigen-related cell adhesion molecule 1


Theoretical massNumber of molelcules
Total (without water)23,7982
Polymers23,7982
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1710 Å2
ΔGint-7 kcal/mol
Surface area10220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.130, 86.060, 66.080
Angle α, β, γ (deg.)90.000, 100.270, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Carcinoembryonic antigen-related cell adhesion molecule 1 / Biliary glycoprotein 1 / BGP-1


Mass: 11899.170 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CEACAM1, BGP, BGP1 / Production host: Escherichia coli (E. coli) / References: UniProt: P13688
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M Ammonium sulfate, 0.1 M HEPES pH 7.5, 25% w/v Polyethylene glycol 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 23, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.2→29.86 Å / Num. obs: 20512 / % possible obs: 100 % / Redundancy: 4.9 % / CC1/2: 0.992 / Rmerge(I) obs: 0.133 / Rpim(I) all: 0.071 / Rrim(I) all: 0.162 / Net I/σ(I): 7.3 / Num. measured all: 101329
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.2-2.324.70.7671399329730.6730.4310.9522.1100
6.96-29.865.10.04634176680.9960.0230.05416.798.9

-
Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Aimless3.3.22data scaling
PDB_EXTRACT3.25data extraction
iMOSFLMdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4QXW

4qxw


Resolution: 2.2→29.86 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2352 / WRfactor Rwork: 0.1832 / FOM work R set: 0.8076 / SU B: 6.447 / SU ML: 0.155 / SU R Cruickshank DPI: 0.2204 / SU Rfree: 0.1942 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.22 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2374 1026 5 %RANDOM
Rwork0.1839 ---
obs0.1866 19486 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 85.85 Å2 / Biso mean: 33.278 Å2 / Biso min: 17.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.85 Å20 Å21.15 Å2
2--1.12 Å2-0 Å2
3----0.65 Å2
Refinement stepCycle: final / Resolution: 2.2→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2520 0 8 74 2602
Biso mean--45.01 33.54 -
Num. residues----321
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0192580
X-RAY DIFFRACTIONr_bond_other_d0.0020.022398
X-RAY DIFFRACTIONr_angle_refined_deg1.7731.943508
X-RAY DIFFRACTIONr_angle_other_deg1.01335494
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8455318
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.73325.682132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.31515405
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.053159
X-RAY DIFFRACTIONr_chiral_restr0.1080.2390
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023012
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02621
LS refinement shellResolution: 2.2→2.257 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 77 -
Rwork0.28 1452 -
all-1529 -
obs--100 %

+
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