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- PDB-4csy: E-selectin lectin, EGF-like and two SCR domains complexed with Si... -

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Entry
Database: PDB / ID: 4csy
TitleE-selectin lectin, EGF-like and two SCR domains complexed with Sialyl Lewis X
ComponentsE-SELECTIN
KeywordsCELL ADHESION / CELL-ADHESION / HUMAN LECTIN / C-TYPE LECTIN / INFLAMMATION / LEUKOCYTE / SIALYL LEWIS X / SLEX / PROTEIN CONFORMATION / LIGAND-INDUCED CONFORMATIONAL CHANGE / 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
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.41 Å
AuthorsPreston, R.C. / Jakob, R.P. / Binder, F.P.C. / Sager, C.P. / Ernst, B. / Maier, T.
CitationJournal: J.Mol.Cell.Biol. / Year: 2016
Title: E-Selectin Ligand Complexes Adopt an Extended High-Affinity Conformation.
Authors: Preston, R.C. / Jakob, R.P. / Binder, F.P. / Sager, C.P. / Ernst, B. / Maier, T.
History
DepositionMar 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _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.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_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.value / _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.pdbx_value_order / _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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Dec 20, 2023Group: 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)67,45820
Polymers62,6122
Non-polymers4,84718
Water2,288127
1
A: E-SELECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72910
Polymers31,3061
Non-polymers2,4239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E-SELECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,72910
Polymers31,3061
Non-polymers2,4239
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.290, 58.670, 58.870
Angle α, β, γ (deg.)76.03, 86.28, 86.31
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.005513, -0.005256), (0.006443, -0.2442, -0.9697), (0.004063, -0.9697, 0.2442)
Vector: -0.365, 1.47536, 1.22574)

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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
Fragment: LECTIN DOMAIN, EGF-LIKE DOMAIN, SHORT CONSENSUS REPEAT DOMAIN 1, SHORT CONSENSUS REPEAT DOMAIN 2, RESIDUES 22-301
Source method: isolated from a genetically manipulated source
Details: N-ACETYLGLUCOSAMINE RESIDUES ATTACHED TO ASN4, ASN124, ASN139, ASN158, ASN178, ASN182, AND ASN244 ON BOTH CHAINS.
Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: CYTOKINE-INDUCED VASCULAR ENDOTHELIAL CELLS / Plasmid: PCDNA3.1
Cell line (production host): CHINESE HAMSTER OVARY (CHO) CELLS
Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: P16581
#2: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)] ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 834.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_1*OC_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4/a3-b1_a4-c1_c3-d2WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}LINUCSPDB-CARE
#3: 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.: 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
#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 / Water


Mass: 18.015 Da / Num. of mol.: 127 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsSIALYL LEWIS X METHYL GLUCOSIDE (DRG): SIALYL-LEWIS-X TETRASACCHARIDE, WITH A TRIMETHYLSILYLETHYL ...SIALYL LEWIS X METHYL GLUCOSIDE (DRG): SIALYL-LEWIS-X TETRASACCHARIDE, WITH A TRIMETHYLSILYLETHYL PROTECTING GROUP, ONLY METHYL GLUCOSIDE WAS MODELED N-ACETYL-D-GLUCOSAMINE (NAG): REMAINS FROM ENDOGLYCOSIDASE H TREATMENT
Sequence detailsWITHOUT N-TERMINAL SECRETION SIGNAL (AA. 1-21). SEQUENCE OF MATURE PROTEIN STARTS WITH RESIDUE 1 ...WITHOUT N-TERMINAL SECRETION SIGNAL (AA. 1-21). SEQUENCE OF MATURE PROTEIN STARTS WITH RESIDUE 1 FOR COMPATIBILITY WITH PREVIOUS E-SELECTIN STRUCTURES (1ESL, 1G1T).

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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: 2.8 Å3/Da / Density % sol: 56.1 % / Description: NONE
Crystal growDetails: 13 % PEG8000, HEPES, MOPS PH 6.2, CACL2, 10MM SLEX-OTMSE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99985
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99985 Å / Relative weight: 1
ReflectionResolution: 2.41→28.28 Å / Num. obs: 25239 / % possible obs: 95.4 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 66.77 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 8.8
Reflection shellResolution: 2.41→2.53 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2 / % possible all: 90.2

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 1G1S, 3GOV, 1H04

1g1s

3gov

1h04


Resolution: 2.41→28.32 Å / Cor.coef. Fo:Fc: 0.9294 / Cor.coef. Fo:Fc free: 0.9003 / SU R Cruickshank DPI: 0.471 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.442 / SU Rfree Blow DPI: 0.261 / SU Rfree Cruickshank DPI: 0.268
Details: DISORDER IN LOOPS 227-231, 254-259 AND N-TERMINAL RESIDUES 278-280 BUILT ACCORDING TO ACCOMPANYING DEPOSITION EBI-57874.
RfactorNum. reflection% reflectionSelection details
Rfree0.2528 1298 5.15 %RANDOM
Rwork0.2148 ---
obs0.2168 25216 96.45 %-
Displacement parametersBiso mean: 79.3 Å2
Baniso -1Baniso -2Baniso -3
1-14.3105 Å2-0.4928 Å2-0.4253 Å2
2---6.6601 Å2-6.0333 Å2
3----7.6504 Å2
Refine analyzeLuzzati coordinate error obs: 0.507 Å
Refinement stepCycle: LAST / Resolution: 2.41→28.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 312 127 4797
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014854HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.226664HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1672SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes135HARMONIC2
X-RAY DIFFRACTIONt_gen_planes694HARMONIC5
X-RAY DIFFRACTIONt_it4854HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.16
X-RAY DIFFRACTIONt_other_torsion17.78
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion704SEMIHARMONIC5
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_contact5465SEMIHARMONIC4
LS refinement shellResolution: 2.41→2.51 Å / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.2629 127 4.49 %
Rwork0.2406 2702 -
all0.2417 2829 -
obs--96.45 %
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)
14.7739-0.42651.28990.2739-0.19910.82430.03990.00260.50590.10540.01370.04370.0801-0.0112-0.0536-0.21040.0168-0.04410.01340.1041-0.15865.521425.9503-13.7994
24.98721.239-0.70440.6541-0.21720.30690.05080.4019-0.2560.1062-0.0762-0.03790.03430.06280.0254-0.2139-0.03140.0332-0.00780.1113-0.0973-5.7848.4486-27.4944
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B

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