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- PDB-1esl: INSIGHT INTO E-SELECTIN(SLASH)LIGAND INTERACTION FROM THE CRYSTAL... -

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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 / sialic acid binding / positive regulation of leukocyte tethering or rolling / oligosaccharide 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 / sialic acid binding / positive regulation of leukocyte tethering or rolling / oligosaccharide 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 / response to tumor necrosis factor / clathrin-coated pit / response to interleukin-1 / response to cytokine / Cell surface interactions at the vascular wall / calcium-mediated signaling / caveola / transmembrane signaling receptor activity / phospholipase C-activating G protein-coupled receptor signaling pathway / 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 ...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 1. / EGF-like domain signature 2. / 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
Revision 1.4Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
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.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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.

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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


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


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
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.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

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

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Data collection

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

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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

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