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- PDB-3cfw: L-selectin lectin and EGF domains -

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Basic information

Entry
Database: PDB / ID: 3cfw
TitleL-selectin lectin and EGF domains
ComponentsL-selectin
KeywordsCELL ADHESION / L-selectin / lectin / EGF / EGF-like domain / Glycoprotein / Membrane / Sushi / Transmembrane
Function / homology
Function and homology information


glycosphingolipid binding / sialic acid binding / oligosaccharide binding / leukocyte tethering or rolling / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / secretory granule membrane / response to cytokine / Cell surface interactions at the vascular wall ...glycosphingolipid binding / sialic acid binding / oligosaccharide binding / leukocyte tethering or rolling / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / secretory granule membrane / response to cytokine / Cell surface interactions at the vascular wall / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / heparin binding / carbohydrate binding / protease binding / cell adhesion / external side of plasma membrane / calcium ion binding / Neutrophil degranulation / extracellular space / plasma membrane
Similarity search - Function
L-selectin / 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 ...L-selectin / 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) / 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: 2.2 Å
AuthorsMehta, P. / Oganesyan, V. / Terzyan, S. / Mather, T. / McEver, R.P.
CitationJournal: J.Biol.Chem. / Year: 2017
Title: Glycan Bound to the Selectin Low Affinity State Engages Glu-88 to Stabilize the High Affinity State under Force.
Authors: Mehta-D'souza, P. / Klopocki, A.G. / Oganesyan, V. / Terzyan, S. / Mather, T. / Li, Z. / Panicker, S.R. / Zhu, C. / McEver, R.P.
History
DepositionMar 4, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 22, 2017Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / 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_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_close_contact / struct_asym / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 30, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_residues
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: L-selectin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3824
Polymers19,2101
Non-polymers1,1723
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.477, 118.477, 118.477
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23

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Components

#1: Protein L-selectin / / Selectin L (Lymphocyte adhesion molecule 1) / isoform CRA_b / Selectin L / Lymphocyte adhesion molecule 1


Mass: 19209.531 Da / Num. of mol.: 1 / Fragment: EGF domain (UNP residues 39-194)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: L-selectin, SELL / Plasmid: pEE14.1 / Cell line (production host): Ovary cells / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Lec 1 / References: UniProt: P14151
#2: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][b-D-Manp]{}}}}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.: 1
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.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / 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: 3.8 Å3/Da / Density % sol: 67.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.17 M Sodium acetate trihydrate, 0.085 M Tris-HCl, pH 8.5, 25.5 % w/v PEG 4000,15% v/v Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12B / Wavelength: 0.9767 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2000 / Details: mirrors/monochromator
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9767 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 14196 / Num. obs: 14192 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 5.25 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 12.8
Reflection shellResolution: 2.2→2.28 Å / Rmerge(I) obs: 0.644 / Mean I/σ(I) obs: 2.32 / Num. unique all: 1402 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ESL

1esl


Resolution: 2.2→25 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2485 686 -random
Rwork0.2006 ---
all-14196 --
obs-13699 96.5 %-
Displacement parametersBiso mean: 34.896 Å2
Refinement stepCycle: LAST / Resolution: 2.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1282 0 76 138 1496
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012531
X-RAY DIFFRACTIONc_angle_deg1.51533
X-RAY DIFFRACTIONc_mcbond_it1.549
X-RAY DIFFRACTIONc_mcangle_it2.584

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