[English] 日本語
Yorodumi
- PDB-1esl: INSIGHT INTO E-SELECTIN(SLASH)LIGAND INTERACTION FROM THE CRYSTAL... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1esl
TitleINSIGHT INTO E-SELECTIN(SLASH)LIGAND INTERACTION FROM THE CRYSTAL STRUCTURE AND MUTAGENESIS OF THE LEC(SLASH)EGF DOMAINS
ComponentsHUMAN E-SELECTIN
KeywordsCELL ADHESION PROTEIN
Function / homology
Function and homology information


actin filament-based process / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / sialic acid binding / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton ...actin filament-based process / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / sialic acid binding / leukocyte migration involved in inflammatory response / leukocyte tethering or rolling / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / cortical cytoskeleton / phospholipase binding / positive regulation of receptor internalization / activation of phospholipase C activity / response to tumor necrosis factor / clathrin-coated pit / response to interleukin-1 / response to cytokine / caveola / calcium-mediated signaling / Cell surface interactions at the vascular wall / transmembrane signaling receptor activity / regulation of inflammatory response / response to lipopolysaccharide / inflammatory response / membrane raft / external side of plasma membrane / perinuclear region of cytoplasm / extracellular space / metal ion binding / plasma membrane
Similarity search - Function
Selectin superfamily / Selectin, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. ...Selectin superfamily / Selectin, C-type lectin-like domain / C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Sushi repeat (SCR repeat) / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/CCP/SCR domain profile. / Sushi/SCR/CCP superfamily / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / EGF-like domain / C-type lectin fold / Epidermal growth factor-like domain. / EGF-like domain profile. / EGF-like domain signature 2. / EGF-like domain signature 1. / EGF-like domain / Roll / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsGraves, B.J. / Crowther, R.L.
Citation
Journal: Nature / Year: 1994
Title: Insight into E-selectin/ligand interaction from the crystal structure and mutagenesis of the lec/EGF domains.
Authors: Graves, B.J. / Crowther, R.L. / Chandran, C. / Rumberger, J.M. / Li, S. / Huang, K.S. / Presky, D.H. / Familletti, P.C. / Wolitzky, B.A. / Burns, D.K.
History
DepositionJun 3, 1994Processing site: BNL
Revision 1.0Aug 31, 1994Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Remark 650HELIX THERE ARE THREE ALPHA-HELICAL TWISTS IN THE STRUCTURE - SEQUENCES IN WHICH THREE CONSECUTIVE ...HELIX THERE ARE THREE ALPHA-HELICAL TWISTS IN THE STRUCTURE - SEQUENCES IN WHICH THREE CONSECUTIVE RESIDUES HAVE HELICAL MAIN CHAIN TORSION ANGLES. TWO OF THESE (VAL 63 - THR 65 AND GLU 71 - ALA 73) ARE RIGHT-HANDED AND HAVE A HYDROGEN BOND FROM THE CARBONYL OF THE RESIDUE PRIOR TO THE TRIAD TO THE AMIDE NITROGEN OF THE RESIDUE JUST AFTER THE TRIPLET. THE OTHER SEQUENCE (CYS 127 - GLY 129) IS LEFT-HANDED WITH TWO HYDROGEN BONDS FROM O SER 126 TO N GLY 129 AND FROM O CYS 127 TO N HIS 130.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: HUMAN E-SELECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7976
Polymers18,6061
Non-polymers1915
Water2,018112
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.380, 73.530, 77.600
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: THERE IS NO DENSITY FOR THE SIDE CHAIN OF RESIDUE GLU 8 BEYOND CB.
2: RESIDUE ASN 58 HAS A GENERALLY WEAK DENSITY BEYOND CB WITH ND2 TOTALLY OUT OF THE DENSITY.
3: ATOM NZ OF RESIDUE LYS 67 IS JUST OUT OF THE SIDE CHAIN DENSITY.
4: THE FOLLOWING ATOMS OF RESIDUE GLU 72 ARE OUT OF DENSITY: CD, OE1 AND OE2.
5: CIS PROLINE - PRO 81
6: THERE IS NO DENSITY FOR THE SIDE CHAIN OF RESIDUE ARG 84 BEYOND CB.
7: THERE IS WEAK DENSITY FOR THE SIDE CHAIN OF RESIDUE GLN 85 BEYOND CB.
8: THERE IS WEAK OR NO DENSITY FOR THE SIDE CHAIN OF RESIDUE GLU 98 BEYOND CB.
9: NO DENSITY FOUND FOR ATOM CD OF RESIDUE LYS 99.
10: RESIDUE ARG 108 HAS A BREAK IN THE DENSITY AT THE CG-CD BOND.
11: NO DENSITY FOUND FOR ATOM NZ OF RESIDUE LYS 112.
12: THE FOLLOWING ATOMS OF RESIDUE ASN 124 ARE OUT OF DENSITY: CG, OD1 AND OD2.
13: NO DENSITY FOUND FOR ATOM CG2 OF RESIDUE THR 125.
14: THERE IS WEAK DENSITY FOR THE SIDE CHAIN OF RESIDUE GLU 132 BEYOND CG.
15: THERE IS WEAK DENSITY FOR THE SIDE CHAIN OF RESIDUE LYS 143 BEYOND CG.
16: THERE IS WEAK DENSITY FOR THE C-TERMINAL CARBOXYLATE, RESIDUE VAL 157.

-
Components

#1: Protein HUMAN E-SELECTIN /


Mass: 18605.820 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: CHO / References: UniProt: P16581
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHREE WATER MOLECULES (HOH 260, HOH 266 AND HOH 318) HAVE TEMPERATURE FACTORS ABOVE 60 A**2 BUT ALL ...THREE WATER MOLECULES (HOH 260, HOH 266 AND HOH 318) HAVE TEMPERATURE FACTORS ABOVE 60 A**2 BUT ALL THREE MAKE GOOD HYDROGEN BONDING CONTACTS TO THE PROTEIN.

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.32 %
Crystal grow
*PLUS
Method: unknown

-
Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2 Å / Rmerge(I) obs: 0.098

-
Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2→10 Å / σ(F): 3
RfactorNum. reflection% reflection
Rfree0.239 --
Rwork0.164 --
all0.173 --
obs-13718 99.8 %
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1266 0 5 112 1383
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.173 / Rfactor obs: 0.164 / Rfactor Rfree: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: x_angle_d / Dev ideal: 2.6

+
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