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- PDB-1g1s: P-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1g1s
TitleP-SELECTIN LECTIN/EGF DOMAINS COMPLEXED WITH PSGL-1 PEPTIDE
Components
  • P-SELECTIN
  • PSGL-1 PEPTIDE
KeywordsIMMUNE SYSTEM / MEMBRANE PROTEIN / selectin / lectin / egf / sulphated / slex
Function / homology
Function and homology information


regulation of integrin activation / leukocyte adhesive activation / fucose binding / glycosphingolipid binding / platelet dense granule membrane / uropod / positive regulation of leukocyte tethering or rolling / sialic acid binding / oligosaccharide binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules ...regulation of integrin activation / leukocyte adhesive activation / fucose binding / glycosphingolipid binding / platelet dense granule membrane / uropod / positive regulation of leukocyte tethering or rolling / sialic acid binding / oligosaccharide binding / calcium-dependent cell-cell adhesion via plasma membrane cell adhesion molecules / platelet alpha granule membrane / leukocyte tethering or rolling / cellular response to interleukin-6 / positive regulation of platelet activation / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte migration / leukocyte cell-cell adhesion / plasma membrane raft / response to cytokine / Cell surface interactions at the vascular wall / lipopolysaccharide binding / cell-cell adhesion / calcium-dependent protein binding / integrin binding / Platelet degranulation / heparin binding / virus receptor activity / defense response to Gram-negative bacterium / response to lipopolysaccharide / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / inflammatory response / external side of plasma membrane / signaling receptor binding / calcium ion binding / extracellular space / membrane / plasma membrane
Similarity search - Function
P-selectin glycoprotein ligand 1 / 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) ...P-selectin glycoprotein ligand 1 / 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 / C-type lectin fold / EGF-like domain profile. / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain / Ribbon / Roll / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
STRONTIUM ION / P-selectin / P-selectin glycoprotein ligand 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsSomers, W.S. / Camphausen, R.T.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2000
Title: Insights into the molecular basis of leukocyte tethering and rolling revealed by structures of P- and E-selectin bound to SLe(X) and PSGL-1.
Authors: Somers, W.S. / Tang, J. / Shaw, G.D. / Camphausen, R.T.
History
DepositionOct 13, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 13, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
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 / database_PDB_caveat / 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_struct_conn_angle / pdbx_validate_chiral / struct_asym / struct_conn / 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_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.type_symbol / _chem_comp.name / _chem_comp.type / _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 / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: P-SELECTIN
B: P-SELECTIN
C: PSGL-1 PEPTIDE
D: PSGL-1 PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01717
Polymers45,5964
Non-polymers3,42113
Water4,035224
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.445, 96.756, 187.289
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

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Protein / Protein/peptide / Sugars , 3 types, 6 molecules ABCD

#1: Protein P-SELECTIN / GRANULE MEMBRANE PROTEIN 140 / GMP-140 / PADGEM / CD62P / LEUKOCYTE-ENDOTHELIAL CELL ADHESION ...GRANULE MEMBRANE PROTEIN 140 / GMP-140 / PADGEM / CD62P / LEUKOCYTE-ENDOTHELIAL CELL ADHESION MOLECULE 3 / LECAM3


Mass: 19131.238 Da / Num. of mol.: 2 / Fragment: LECTIN/EGF DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16109
#2: Protein/peptide PSGL-1 PEPTIDE / PSGL-1


Mass: 3666.835 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): CHO CELLS / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q14242
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2- ...N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-[beta-D-galactopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-galactopyranose


Type: oligosaccharide / Mass: 1186.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4[LFucpa1-3]DGlcpNAcb1-6[DGalpb1-3]DGalpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,6,5/[a2112h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3-4-2-5/a3-b1_a6-c1_c3-d1_c4-e1_e3-f2WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 235 molecules

#4: Chemical ChemComp-SR / STRONTIUM ION


Mass: 87.620 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Sr
#5: Chemical
ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.15 Å3/Da / Density % sol: 60.96 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 100 mM HEPES, 10 mM TRIS, 150 mN NaCl, 4 mM CaCl2, 50 mM SrCl2, 5% PEG 6000, 33% MPD, pH 7.0, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
2100 mMHEPES1drop
310 mMTris-HCl1drop
4150 mM1dropNaCl
54 mM1dropCaCl2
650 mM1dropSrCl2
75 %(w/v)PEG60001drop
833 %(v/v)MPD1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.99987 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1997
RadiationMonochromator: synchrotron / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 44923 / Num. obs: 44923 / % possible obs: 98.5 % / Observed criterion σ(I): 3 / Redundancy: 4.63 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 25.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.63 % / Rmerge(I) obs: 0.274 / Mean I/σ(I) obs: 3.7 / % possible all: 96.6
Reflection
*PLUS
Num. measured all: 207998
Reflection shell
*PLUS
% possible obs: 96.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
CNSrefinement
RefinementMethod to determine structure: MIR
Starting model: P-selectin

Resolution: 1.9→15 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.235 2246 5 %random
Rwork0.204 ---
all0.204 44923 --
obs0.204 44923 --
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2814 0 220 224 3258
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.54
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.01

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