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- PDB-1uh1: Crystal structure of jacalin- GalNAc-beta(1-3)-Gal-alpha-O-Me complex -

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Basic information

Entry
Database: PDB / ID: 1uh1
TitleCrystal structure of jacalin- GalNAc-beta(1-3)-Gal-alpha-O-Me complex
Components
  • Agglutinin alpha chain
  • Agglutinin beta-3 chain
KeywordsSUGAR BINDING PROTEIN / All beta sheet protein / Beta-prism I fold / Gal specific
Function / homology
Function and homology information


IgA binding / carbohydrate binding
Similarity search - Function
Jacalin-like lectin domain, plant / Jacalin-like lectin domain / Jacalin-like lectin domain / Jacalin-like lectin domain / Aligned Prism / Vitelline Membrane Outer Layer Protein I, subunit A / Jacalin-like lectin domain / Jacalin-type lectin domain profile. / Jacalin-like lectin domain superfamily / Mainly Beta
Similarity search - Domain/homology
Chem-MGC / Agglutinin alpha chain / Agglutinin beta-3 chain
Similarity search - Component
Biological speciesArtocarpus integer (campedak)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsJeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
Citation
Journal: J.MOL.BIOL. / Year: 2003
Title: Structural Basis of the Carbohydrate Specificities of Jacalin: An X-ray and Modeling Study
Authors: Jeyaprakash, A.A. / Katiyar, S. / Swaminathan, C.P. / Sekar, K. / Surolia, A. / Vijayan, M.
#1: Journal: J.Mol.Biol. / Year: 2002
Title: Crystal structure of the jacalin-T-antigen complex and a comparative study of lectin-T-antigen complexes
Authors: Jeyaprakash, A.A. / Rani, P.G. / Reddy, G.B. / Banumathi, S. / Betzel, C. / Sekar, K. / Surolia, A. / Vijayan, M.
#2: Journal: Nat.Struct.Biol. / Year: 1996
Title: A Novel mode of carbohydrate recognition in jacalin, A moraceae plant lectin with a beta-prism fold
Authors: Sankaranarayanan, R. / Sekar, K. / Banerjee, R. / Sharma, V. / Surolia, A. / Vijayan, M.
History
DepositionJun 23, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / 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 / 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_special_symmetry / pdbx_validate_close_contact / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 25, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,42212
Polymers66,9958
Non-polymers1,4274
Water2,162120
1
A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,26012
Polymers66,9958
Non-polymers1,2654
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_555-x+y,y,-z+1/21
Buried area14220 Å2
ΔGint-64 kcal/mol
Surface area23690 Å2
MethodPISA, PQS
2
E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules

E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,58512
Polymers66,9958
Non-polymers1,5904
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_666-y+1,-x+1,-z+7/61
Buried area15090 Å2
ΔGint-49 kcal/mol
Surface area23420 Å2
MethodPISA, PQS
3
E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,55318
Polymers100,49312
Non-polymers2,0606
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z+2/31
crystal symmetry operation12_555x,x-y,-z+5/61
Buried area26580 Å2
ΔGint-69 kcal/mol
Surface area49840 Å2
MethodPISA
4
E: Agglutinin alpha chain
F: Agglutinin beta-3 chain
G: Agglutinin alpha chain
H: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules

A: Agglutinin alpha chain
B: Agglutinin beta-3 chain
C: Agglutinin alpha chain
D: Agglutinin beta-3 chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,55318
Polymers100,49312
Non-polymers2,0606
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_655x-y+1,x,z+5/61
crystal symmetry operation8_666x-y+1,-y+1,-z+11
Buried area24620 Å2
ΔGint-59 kcal/mol
Surface area51800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)129.446, 129.446, 158.346
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11E-222-

HOH

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Components

#1: Protein
Agglutinin alpha chain / jacalin alpha chain


Mass: 14673.479 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seedsSeed / References: UniProt: P18670
#2: Protein/peptide
Agglutinin beta-3 chain / jacalin beta-3 chain


Mass: 2075.279 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Artocarpus integer (campedak) / Organ: seedsSeed / References: UniProt: P18673
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-galactopyranose-(1-3)-methyl alpha-D-galactopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpNAcb1-3DGalp[1Me]a1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_1*OC][a2112h-1b_1-5_2*NCC/3=O]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][a-D-Galp]{[(3+1)][b-D-GalpNAc]{}}}LINUCSPDB-CARE
#4: Sugar ChemComp-MGC / methyl 2-acetamido-2-deoxy-alpha-D-galactopyranoside / ALPHA-METHYL-N-ACETYL-D-GALACTOSAMINE / methyl 2-acetamido-2-deoxy-alpha-D-galactoside / methyl 2-acetamido-2-deoxy-D-galactoside / methyl 2-acetamido-2-deoxy-galactoside / Methyl group


Type: D-saccharide / Mass: 235.234 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C9H17NO6
IdentifierTypeProgram
DGalpNAc[1Me]aCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
1-methyl-N-acetyl-a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-methyl-N-acetyl-D-galactosamineIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 120 / 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: 2.85 Å3/Da / Density % sol: 56.49 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: PEG 4000, NaCl, sodium azide, Phosphate buffer, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
20.02 Mphosphate1droppH7.3
30.1 M1dropNaCl
40.025 %(w/v)sodium azide1drop
58-10 %PEG40001drop
640 %PEG40001reservoir

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: Osmic mirror
RadiationMonochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 19332 / Num. obs: 19332 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Biso Wilson estimate: 46.8 Å2 / Rmerge(I) obs: 0.119
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.464 / Num. unique all: 1860 / % possible all: 97
Reflection
*PLUS
Lowest resolution: 20 Å / Num. measured all: 81752
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 97 % / Num. unique obs: 1860

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1JAC

1jac


Resolution: 2.8→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 184866.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 919 4.9 %RANDOM
Rwork0.192 ---
obs0.192 18669 95.1 %-
all-18869 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.1104 Å2 / ksol: 0.297384 e/Å3
Displacement parametersBiso mean: 39.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.96 Å20.6 Å20 Å2
2--0.96 Å20 Å2
3----1.91 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.55 Å0.47 Å
Refinement stepCycle: LAST / Resolution: 2.8→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4584 0 97 120 4801
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d26.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it4.721.5
X-RAY DIFFRACTIONc_mcangle_it7.362
X-RAY DIFFRACTIONc_scbond_it8.352
X-RAY DIFFRACTIONc_scangle_it12.12.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.97 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.361 151 5.1 %
Rwork0.302 2828 -
obs--92.7 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM
X-RAY DIFFRACTION2CIS1.PARAM
X-RAY DIFFRACTION3WATER_REP.PARAM
X-RAY DIFFRACTION4CARBOHYDRATE.PARAM
X-RAY DIFFRACTION5JACSOAK.PARAM
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.8

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