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

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Basic information

Entry
Database: PDB / ID: 6eyj
TitleE-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic ligand NV354
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 / positive regulation of leukocyte tethering or rolling / sialic acid binding / 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 / positive regulation of leukocyte tethering or rolling / sialic acid binding / 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 / positive regulation of receptor internalization / phospholipase binding / 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 / : / Complement Module, domain 1 / Complement Module; domain 1 / 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) ...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. / 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) / 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-C5H / E-selectin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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_asym_id / _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.ptnr2_auth_asym_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
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: E-selectin
B: E-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,05420
Polymers62,6122
Non-polymers4,44218
Water4,540252
1
A: E-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,52710
Polymers31,3061
Non-polymers2,2219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: E-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,52710
Polymers31,3061
Non-polymers2,2219
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.580, 71.040, 92.160
Angle α, β, γ (deg.)90.00, 93.73, 90.00
Int Tables number4
Space group name H-MP1211

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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.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SELE, ELAM1 / Plasmid: pCDNA3.1 / Cell line (production host): CHO / 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 14
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-C5H / (2~{S})-3-cyclohexyl-2-[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-3,5-bis(oxidanyl)-6-[(1~{R},2~{R})-2-[(2~{R},3~{S},4~{R},5~{S},6~{R})-3,4,5-tris(oxidanyl)-6-(trifluoromethyl)oxan-2-yl]oxycyclohexyl]oxy-oxan-4-yl]oxy-propanoic acid


Mass: 632.618 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H43F3O13
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.16 %
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: 1.00003 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 6, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.2→56.22 Å / Num. obs: 33972 / % possible obs: 98.3 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.1 Å2 / CC1/2: 0.982 / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.809 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 3343 / CC1/2: 0.612 / % possible all: 97.1

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Processing

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

4c16


Resolution: 2.2→56.22 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 0 / SU R Blow DPI: 0.286 / SU Rfree Blow DPI: 0.216 / SU Rfree Cruickshank DPI: 0.216
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1650 4.86 %RANDOM
Rwork0.219 ---
obs0.221 33972 98.3 %-
Displacement parametersBiso mean: 63.62 Å2
Baniso -1Baniso -2Baniso -3
1-12.4832 Å20 Å2-1.1862 Å2
2---3.9006 Å20 Å2
3----8.5826 Å2
Refine analyzeLuzzati coordinate error obs: 0.37 Å
Refinement stepCycle: 1 / Resolution: 2.2→56.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 284 244 4886
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094792HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.126564HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2172SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes134HARMONIC2
X-RAY DIFFRACTIONt_gen_planes680HARMONIC5
X-RAY DIFFRACTIONt_it4792HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.4
X-RAY DIFFRACTIONt_other_torsion2.89
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion682SEMIHARMONIC5
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_contact5302SEMIHARMONIC4
LS refinement shellResolution: 2.2→2.27 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.2837 132 4.57 %
Rwork0.2663 2756 -
all0.2671 2888 -
obs--97.41 %
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)
19.1645-4.3259-2.13153.49161.10453.9414-0.2648-0.3476-0.2836-0.19840.07320.1802-0.2966-0.41810.1916-0.25930.0761-0.038-0.0897-0.0768-0.1406-14.2179-52.804279.819
23.734-1.36990.59752.04322.34727.44360.0726-0.33250.473-0.3386-0.16640.3194-1.0634-0.26810.0938-0.09070.1559-0.0460.037-0.09280.108-17.3631-42.255187.3866
37.7062-5.4244-0.15172.02390.36770.7059-0.0822-0.1297-0.22080.1755-0.0123-0.0917-0.0870.19280.0945-0.38960.04390.0017-0.10360.05270.401213.1857-66.344276.9954
410.4039-3.49753.377101.00270.4578-0.0509-0.1061-0.05950.02690.0560.28760.02670.3409-0.0051-0.4270.07120.0684-0.02070.23030.339837.5237-77.234978.4086
512.3672-0.08673.15538.41192.93913.85780.2356-0.3439-1.219-0.05990.3805-1.64010.3191-0.0139-0.6161-0.39810.06170.095-0.28420.18120.509672.3941-90.551177.0689
69.34812.8803-2.01863.2186-0.06663.08560.14250.04570.16070.2919-0.1662-0.3496-0.13040.02460.0237-0.2167-0.0383-0.0304-0.29770.1354-0.14075.27-51.250759.9256
74.03150.9011-1.18125.4054-0.66747.84670.38410.23870.83020.3484-0.17180.0308-1.3003-0.2117-0.2122-0.0374-0.02590.0797-0.26430.13270.04998.5288-40.040953.6483
812.97025.85711.1831.27910.27520.31030.0582-0.0347-0.6111-0.0710.08730.1074-0.0828-0.1798-0.1455-0.283-0.0588-0.0221-0.20580.04620.4721-22.1718-65.155460.7764
95.25741.24731.7700.04890.20840.0117-0.4772-0.5143-0.1403-0.2215-0.46420.007-0.19330.2098-0.2997-0.05840.0216-0.1823-0.02920.4508-46.5701-75.570157.8292
1010.57310.5225.49589.02050.15644.68860.05880.1694-1.09670.13370.18631.51640.2475-0.262-0.2451-0.1564-0.04270.0939-0.1971-0.01380.5098-81.518-89.011456.4812
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|1 - A|52 }
2X-RAY DIFFRACTION2{ A|53 - A|115 }
3X-RAY DIFFRACTION3{ A|116 - A|167 }
4X-RAY DIFFRACTION4{ A|168 - A|218 }
5X-RAY DIFFRACTION5{ A|219 - A|280 }
6X-RAY DIFFRACTION6{ B|1 - B|52 }
7X-RAY DIFFRACTION7{ B|53 - B|115 }
8X-RAY DIFFRACTION8{ B|116 - B|167 }
9X-RAY DIFFRACTION9{ B|168 - B|218 }
10X-RAY DIFFRACTION10{ B|219 - B|280 }

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