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- PDB-6eyi: E-selectin lectin, EGF-like and two SCR domains complexed with gl... -

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Basic information

Entry
Database: PDB / ID: 6eyi
TitleE-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand BW69669
ComponentsE-selectin
KeywordsCELL ADHESION / CELL-ADHESION MOLECULE / C-TYPE LECTIN / INFLAMMATION / LEUKOCYTE / GLYCOMIMETIC / CATCH-BOND
Function / homology
Function and homology information


actin filament-based process / sialic acid binding / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / 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 / oligosaccharide binding / positive regulation of leukocyte tethering or rolling / 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 / Complement Module, domain 1 / Complement Module; domain 1 / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) ...Selectin superfamily / Selectin, C-type lectin-like domain / Complement Module, domain 1 / Complement Module; domain 1 / C-type lectin, conserved site / C-type lectin domain signature. / Sushi repeat (SCR repeat) / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Domain abundant in complement control proteins; SUSHI repeat; short complement-like repeat (SCR) / Sushi/SCR/CCP domain / Sushi/SCR/CCP superfamily / Sushi/CCP/SCR domain profile. / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / Laminin / Laminin / 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 / Ribbon / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-C4Z / E-selectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsJakob, R.P. / Zihlmann, P. / Preston, R.C. / Varga, N. / Ernst, B. / Maier, T.
CitationJournal: To Be Published
Title: E-selectin lectin with different glycomimetic ligands
Authors: Varga, N. / Zihlmann, P. / Preston, R.C. / Jakob, R.P. / Maier, T. / Ernst, B.
History
DepositionNov 13, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,55312
Polymers31,3061
Non-polymers2,24711
Water2,288127
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1700 Å2
ΔGint12 kcal/mol
Surface area17840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.590, 72.940, 52.520
Angle α, β, γ (deg.)90.00, 94.16, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-405-

HOH

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Components

#1: Protein E-selectin / / CD62 antigen-like family member E / Endothelial leukocyte adhesion molecule 1 / ELAM-1 / Leukocyte- ...CD62 antigen-like family member E / Endothelial leukocyte adhesion molecule 1 / ELAM-1 / Leukocyte-endothelial cell adhesion molecule 2 / LECAM2


Mass: 31305.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SELE, ELAM1 / Plasmid: PCDNA3.1 / Cell (production host): CHO / Organ (production host): OVARY / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16581
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 7
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-C4Z / (2~{R})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-[(1~{R},2~{R})-2-[(2~{S},3~{S},4~{R},5~{S},6~{S})-6-methyl-3,4,5-tris(oxidanyl)oxan-2-yl]oxycyclohexyl]oxy-3,5-bis(oxidanyl)oxan-4-yl]oxy-propanoic acid


Mass: 578.646 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H46O13
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 56.93 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2M CaCl2, 0.1 M Mops pH 6.2, 11-14% PEG8000, after microseeding

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99999 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99999 Å / Relative weight: 1
ReflectionResolution: 2.04→57.3 Å / Num. obs: 21493 / % possible obs: 95.6 % / Redundancy: 3.3 % / Biso Wilson estimate: 52.7 Å2 / CC1/2: 0.966 / Rmerge(I) obs: 0.148 / Net I/σ(I): 16.1
Reflection shellResolution: 2.04→2.12 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.849 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 2035 / CC1/2: 0.795 / % possible all: 92.2

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4C16

4c16


Resolution: 2.04→20.76 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.924 / SU R Cruickshank DPI: 0.211 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.214 / SU Rfree Blow DPI: 0.165 / SU Rfree Cruickshank DPI: 0.165
RfactorNum. reflection% reflectionSelection details
Rfree0.237 985 4.58 %RANDOM
Rwork0.224 ---
obs0.225 21493 95.6 %-
Displacement parametersBiso mean: 71.97 Å2
Baniso -1Baniso -2Baniso -3
1--16.7933 Å20 Å2-2.0572 Å2
2---0.7506 Å20 Å2
3---17.5439 Å2
Refine analyzeLuzzati coordinate error obs: 0.38 Å
Refinement stepCycle: 1 / Resolution: 2.04→20.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2179 0 141 130 2450
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082393HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.083276HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1085SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes340HARMONIC5
X-RAY DIFFRACTIONt_it2393HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.3
X-RAY DIFFRACTIONt_other_torsion2.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion328SEMIHARMONIC5
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_contact2741SEMIHARMONIC4
LS refinement shellResolution: 2.04→2.14 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2661 116 4.39 %
Rwork0.2569 2529 -
all0.2573 2645 -
obs--89.31 %
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)
19.01181.7812-1.075210.6180.14647.98790.2143-0.38950.27960.2668-0.0829-0.0789-0.3658-0.2842-0.1314-0.2239-0.09010.0397-0.19430.0574-0.1996-16.3571-15.901137.3155
26.7651.5797-1.76532.212-0.51113.30050.1387-0.2918-1.09110.3048-0.2681-0.47790.4665-0.10930.1294-0.1392-0.1037-0.039-0.27960.1497-0.0357-17.0613-29.513937.1267
30.82081.0783-1.41722.0484-5.75789.20480.00550.17090.0135-0.07550.18060.3447-0.5528-0.0526-0.18610.2771-0.04650.0145-0.16640.0648-0.2108-8.7196-6.14237.8448
41.45520.16890.397100.12298.35540.11960.29630.05280.43420.01480.24220.1456-0.4078-0.13440.1247-0.02270.0333-0.13350.0561-0.2753-9.18534.6162-16.6594
53.46081.87643.75459.1516-1.80747.7654-0.38580.13930.296-1.07010.571-0.2921-1.0993-0.0154-0.18520.0910.02190.1314-0.29290.07-0.3193-6.294717.9987-51.697
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|4 - A|31 }
2X-RAY DIFFRACTION2{ A|32 - A|115 }
3X-RAY DIFFRACTION3{ A|116 - A|167 }
4X-RAY DIFFRACTION4{ A|168 - A|218 }
5X-RAY DIFFRACTION5{ A|219 - A|280 }

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