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- PDB-1g1q: Crystal structure of P-selectin lectin/EGF domains -

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Basic information

Entry
Database: PDB / ID: 1g1q
TitleCrystal structure of P-selectin lectin/EGF domains
ComponentsP-SELECTIN
KeywordsIMMUNE SYSTEM / MEMBRANE PROTEIN / Lectin / EGF / Adhesion molecule
Function / homology
Function and homology information


regulation of integrin activation / fucose binding / glycosphingolipid binding / platelet dense granule membrane / 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 ...regulation of integrin activation / fucose binding / glycosphingolipid binding / platelet dense granule membrane / 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 / positive regulation of platelet activation / positive regulation of leukocyte migration / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / leukocyte cell-cell adhesion / 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 / 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 / calcium ion binding / extracellular space / plasma membrane
Similarity search - Function
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 ...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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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: Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.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.pdbx_dist_value / _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_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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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: P-SELECTIN
D: P-SELECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,92210
Polymers76,5254
Non-polymers3976
Water2,414134
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.0, 60.83, 91.440
Angle α, β, γ (deg.)90.00, 103.58, 90.00
Int Tables number4
Cell settingmonoclinic
Space group name H-MP1211

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Components

#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.: 4 / Fragment: LECTIN/EGF DOMAINS
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): ovary [CHO] cells / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P16109
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.86 Å3/Da / Density % sol: 57 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Tris-HCl, NaCl, CaCl2, 2-methyl-2,4-pentanediol, PEG 6000, pH 8.5, VAPOR DIFFUSION, HANGING DROP at 291K
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
2100 mMTris-HCl1drop
3150 mM1dropNaCl
412 mM1dropCaCl2
510 %(v/v)MPD1drop
610 %(w/v)PEG60001drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jan 1, 1995 / Details: Yale/MSC mirrors
RadiationMonochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→15 Å / Num. all: 32570 / Num. obs: 32570 / % possible obs: 95.8 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 3 / Redundancy: 7.3798 % / Biso Wilson estimate: 20 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 35.7
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 7.3798 % / Rmerge(I) obs: 0.225 / % possible all: 74.2
Reflection
*PLUS
Num. measured all: 240361
Reflection shell
*PLUS
% possible obs: 74.2 % / Mean I/σ(I) obs: 6.6

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→14 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1628 5 %random
Rwork0.213 ---
all0.213 32570 --
obs0.213 32570 --
Refinement stepCycle: LAST / Resolution: 2.4→14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5264 0 4 150 5418
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d1.46
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 14 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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