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- PDB-4q56: Structure of Helix aspersa agglutinin with natural glycosylation ... -

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Basic information

Entry
Database: PDB / ID: 4q56
TitleStructure of Helix aspersa agglutinin with natural glycosylation and N-acetyl-alpha-D-galactosamine (GalNAc)
ComponentsHelix aspersa agglutinin (HAA)
KeywordsSUGAR BINDING PROTEIN / CARBOHYDRATE-BINDING PROTEIN / H-TYPE LECTIN / SNAIL MUCUS
Function / homology
Function and homology information


carbohydrate binding / cell adhesion / metal ion binding
Similarity search - Function
Immunoglobulin-like - #2080 / H-type lectin domain / H-type lectin domain superfamily / H-type lectin domain / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
2-acetamido-2-deoxy-alpha-D-galactopyranose / ACETATE ION / Helix aspersa agglutinin (HAA)
Similarity search - Component
Biological speciesHelix aspersa (brown garden snail)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.38 Å
AuthorsPietrzyk, A.J. / Bujacz, A. / Bujacz, G.
CitationJournal: Int.J.Biol.Macromol. / Year: 2015
Title: Structural studies of Helix aspersa agglutinin complexed with GalNAc: A lectin that serves as a diagnostic tool.
Authors: Pietrzyk, A.J. / Bujacz, A. / Mak, P. / Potempa, B. / Niedziela, T.
History
DepositionApr 16, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 14, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 28, 2015Group: Database references
Revision 1.2Mar 7, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 2.0Dec 25, 2019Group: Data collection / Derived calculations / Polymer sequence
Category: chem_comp / entity_poly ...chem_comp / entity_poly / pdbx_struct_mod_residue / struct_conn
Item: _chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can ..._chem_comp.type / _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_struct_conn_angle / pdbx_struct_special_symmetry / 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.occupancy / _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.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _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_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_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_struct_special_symmetry.label_asym_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Helix aspersa agglutinin (HAA)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7556
Polymers11,3461
Non-polymers1,4105
Water2,144119
1
A: Helix aspersa agglutinin (HAA)
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)76,53236
Polymers68,0756
Non-polymers8,45830
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation16_545y+1/3,x-1/3,-z+2/31
crystal symmetry operation17_555x-y+1/3,-y+2/3,-z+2/31
crystal symmetry operation18_655-x+4/3,-x+y+2/3,-z+2/31
Buried area15320 Å2
ΔGint-51 kcal/mol
Surface area33850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.900, 47.900, 281.530
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-203-

NA

21A-210-

ZN

31A-337-

HOH

41A-396-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Helix aspersa agglutinin (HAA)


Mass: 11345.768 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Helix aspersa (brown garden snail) / References: UniProt: A0A0R4I963*PLUS

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Sugars , 2 types, 2 molecules

#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-[beta-D- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-alpha-L-fucopyranose-(1-3)-[beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1040.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2DGalpb1-4LFucpa1-3[DManpb1-4DGlcpNAcb1-4]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5][a1122h-1b_1-5]/1-2-3-2-1-4/a3-b1_a4-e1_b4-c1_c2-d1_e4-f1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#4: Sugar ChemComp-A2G / 2-acetamido-2-deoxy-alpha-D-galactopyranose / N-acetyl-alpha-D-galactosamine / 2-acetamido-2-deoxy-alpha-D-galactose / 2-acetamido-2-deoxy-D-galactose / 2-acetamido-2-deoxy-galactose / N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGalpNAcaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-a-D-galactopyranosamineCOMMON NAMEGMML 1.0
a-D-GalpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 122 molecules

#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.74 Å3/Da / Density % sol: 55.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.05 M Zn(CH3COO)2, 0.1 M HEPES, pH 7.0, 40% MPD, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.967 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 30, 2013 / Details: mirrors
RadiationMonochromator: Double-crystal Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.967 Å / Relative weight: 1
ReflectionResolution: 1.38→46.92 Å / Num. all: 25294 / Num. obs: 25294 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.54 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 29.35
Reflection shellResolution: 1.38→1.48 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.0114 / Mean I/σ(I) obs: 2.54 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
XDSdata scaling
PHASERphasing
REFMAC5.7.0032refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2CCV

2ccv


Resolution: 1.38→46.92 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / SU B: 1.97 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.049 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16782 1083 4.1 %RANDOM
Rwork0.13658 ---
obs0.13788 25294 99.95 %-
all-25294 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.068 Å2
Baniso -1Baniso -2Baniso -3
1-0.59 Å20.59 Å2-0 Å2
2--0.59 Å20 Å2
3----1.93 Å2
Refinement stepCycle: LAST / Resolution: 1.38→46.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms796 0 91 119 1006
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.02948
X-RAY DIFFRACTIONr_bond_other_d0.0020.02874
X-RAY DIFFRACTIONr_angle_refined_deg2.0132.0681309
X-RAY DIFFRACTIONr_angle_other_deg0.8763.0022013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5575112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.93924.05437
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.46315147
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.175156
X-RAY DIFFRACTIONr_chiral_restr0.1210.2167
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021994
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02197
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9362.785416
X-RAY DIFFRACTIONr_mcbond_other2.8972.769414
X-RAY DIFFRACTIONr_mcangle_it3.614.161520
X-RAY DIFFRACTIONr_mcangle_other4.1454.331513
X-RAY DIFFRACTIONr_scbond_it4.4313.169529
X-RAY DIFFRACTIONr_scbond_other4.8353.195511
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.3974.744758
X-RAY DIFFRACTIONr_long_range_B_refined6.83425.3751045
X-RAY DIFFRACTIONr_long_range_B_other5.30124.168989
X-RAY DIFFRACTIONr_rigid_bond_restr5.08231818
X-RAY DIFFRACTIONr_sphericity_free29.808549
X-RAY DIFFRACTIONr_sphericity_bonded14.73451862
LS refinement shellResolution: 1.38→1.416 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 73 -
Rwork0.299 1843 -
obs--99.95 %

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