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- PDB-4c16: E-selectin lectin, EGF-like and two SCR domains complexed with gl... -

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Basic information

Entry
Database: PDB / ID: 4c16
TitleE-selectin lectin, EGF-like and two SCR domains complexed with glycomimetic antagonist
ComponentsE-SELECTIN
KeywordsCELL ADHESION / CELL-ADHESION MOLECULE / C-TYPE LECTIN / INFLAMMATION / LEUKOCYTE / GLYCOMIMETIC / ANTAGONIST / 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
(S)-CYCLOHEXYL LACTIC ACID / alpha-L-fucopyranose / beta-D-galactopyranose / (1R,2R,3S)-3-methylcyclohexane-1,2-diol / E-selectin
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 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
DepositionAug 9, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 20, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 8, 2015Group: Database references
Revision 1.2Jan 27, 2016Group: Database references
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _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.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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Dec 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
Remark 700 SHEET DETERMINATION METHOD: AUTHOR PROVIDED.

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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)67,08226
Polymers62,6122
Non-polymers4,47124
Water9,458525
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A: E-SELECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54113
Polymers31,3061
Non-polymers2,23512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: E-SELECTIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,54113
Polymers31,3061
Non-polymers2,23512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.582, 56.917, 59.684
Angle α, β, γ (deg.)74.40, 87.11, 88.26
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-1, -0.008697, -0.001289), (0.003593, -0.2704, -0.9627), (0.008024, -0.9627, 0.2704)
Vector: -0.22542, 1.92032, 1.68025)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein E-SELECTIN / / CD62 ANTIGEN-LIKE FAMILY MEMBER E / ENDOTHELIAL LEUKOCYTE AD HESION MOLECULE 1 / ELAM-1 / LEUKOCYTE- ...CD62 ANTIGEN-LIKE FAMILY MEMBER E / ENDOTHELIAL LEUKOCYTE AD HESION MOLECULE 1 / ELAM-1 / LEUKOCYTE-ENDOTHELIAL CELL ADHESION MOL ECULE 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, RESDIUES 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 / Production host: CRICETULUS GRISEUS (Chinese hamster) / Tissue (production host): OVARY / References: UniProt: P16581

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Sugars , 3 types, 18 molecules

#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 / 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
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#7: Sugar ChemComp-FUC / alpha-L-fucopyranose / alpha-L-fucose / 6-deoxy-alpha-L-galactopyranose / L-fucose / fucose / Fucose


Type: L-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
LFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-L-fucopyranoseCOMMON NAMEGMML 1.0
a-L-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 531 molecules

#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-4WC / (S)-CYCLOHEXYL LACTIC ACID


Mass: 172.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16O3
#6: Chemical ChemComp-Q6Z / (1R,2R,3S)-3-methylcyclohexane-1,2-diol


Mass: 130.185 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H14O2
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 525 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details{(1R,2R, 3S)-2-[(ALPHA-L-FUCOPYRANOSYL)OXY]-3-METHYL-CYCLOHEX-1-YL} 3-O- [SODIUM (1S)-1-CARBOXY-2- ...{(1R,2R, 3S)-2-[(ALPHA-L-FUCOPYRANOSYL)OXY]-3-METHYL-CYCLOHEX-1-YL} 3-O- [SODIUM (1S)-1-CARBOXY-2-CYCLOHEXYL-ETHYL]-BETA-D-GALACTOPYRANOSIDE MADE UP OF 4WC-GAL-Q6Z-FUC
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: 2.75 Å3/Da / Density % sol: 55.36 % / Description: NONE
Crystal growDetails: PEG8000, HEPES, MOPS PH 6.2, CACL2, ANTAGONIST

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.99987
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 6, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99987 Å / Relative weight: 1
ReflectionResolution: 1.93→57.43 Å / Num. obs: 50213 / % possible obs: 92.5 % / Observed criterion σ(I): 2 / Redundancy: 1.8 % / Biso Wilson estimate: 33.92 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 9.3
Reflection shellResolution: 1.93→2.03 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2 / % possible all: 90.7

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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: 1.93→15.81 Å / Cor.coef. Fo:Fc: 0.9325 / Cor.coef. Fo:Fc free: 0.9005 / SU R Cruickshank DPI: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.172 / SU Rfree Blow DPI: 0.158 / SU Rfree Cruickshank DPI: 0.156
RfactorNum. reflection% reflectionSelection details
Rfree0.2324 2332 5.04 %RANDOM
Rwork0.1803 ---
obs0.183 46243 92.54 %-
Displacement parametersBiso mean: 41.26 Å2
Baniso -1Baniso -2Baniso -3
1-13.2274 Å21.1292 Å20.281 Å2
2---9.6056 Å2-8.2346 Å2
3----3.6218 Å2
Refine analyzeLuzzati coordinate error obs: 0.248 Å
Refinement stepCycle: LAST / Resolution: 1.93→15.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4358 0 280 525 5163
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015028HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.166919HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1756SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes139HARMONIC2
X-RAY DIFFRACTIONt_gen_planes735HARMONIC5
X-RAY DIFFRACTIONt_it5028HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.44
X-RAY DIFFRACTIONt_other_torsion16.97
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion684SEMIHARMONIC5
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_contact6289SEMIHARMONIC4
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2856 177 5.27 %
Rwork0.2431 3180 -
all0.2453 3357 -
obs--92.54 %

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