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- PDB-5e98: Crystal structure of human heparanase in complex with HepMer M04S02a -

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Entry
Database: PDB / ID: 5.0E+98
TitleCrystal structure of human heparanase in complex with HepMer M04S02a
Components(Heparanase) x 2
KeywordsHYDROLASE / glycoside hydrolase / heparan / protein / sugar
Function / homology
Function and homology information


heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process ...heparanase / heparanase activity / regulation of hair follicle development / heparin proteoglycan metabolic process / heparan sulfate proteoglycan catabolic process / beta-glucuronidase activity / HS-GAG degradation / positive regulation of hair follicle development / syndecan binding / proteoglycan metabolic process / vascular wound healing / protein transmembrane transport / establishment of endothelial barrier / angiogenesis involved in wound healing / positive regulation of osteoblast proliferation / positive regulation of vascular endothelial growth factor production / positive regulation of blood coagulation / extracellular matrix / lysosomal lumen / cell-matrix adhesion / specific granule lumen / lysosome / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / membrane raft / lysosomal membrane / response to antibiotic / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular space / extracellular region / nucleoplasm / nucleus
Similarity search - Function
Glycoside hydrolase, family 79 / Glycosyl hydrolase family 79, N-terminal domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
IMIDAZOLE / P-NITROPHENOL / Heparanase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.63 Å
AuthorsWu, L. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)AdG 322942 United Kingdom
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2015
Title: Structural characterization of human heparanase reveals insights into substrate recognition.
Authors: Wu, L. / Viola, C.M. / Brzozowski, A.M. / Davies, G.J.
History
DepositionOct 14, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Dec 16, 2015Group: Database references
Revision 2.0Jul 15, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Category: atom_site / atom_sites ...atom_site / atom_sites / atom_type / chem_comp / computing / diffrn / entity / pdbx_audit_support / pdbx_database_related / pdbx_database_status / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / pdbx_validate_rmsd_bond / pdbx_validate_torsion / pdbx_version / refine / refine_hist / refine_ls_restr / refine_ls_shell / reflns / reflns_shell / software / struct / struct_asym / struct_conf / struct_conn / struct_keywords / struct_mon_prot_cis / struct_site / struct_site_gen
Item: _atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] ..._atom_sites.fract_transf_matrix[2][1] / _atom_sites.fract_transf_matrix[3][2] / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _diffrn.pdbx_serial_crystal_experiment / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number / _pdbx_database_status.deposit_site / _pdbx_struct_assembly.details / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _refine.B_iso_mean / _refine.aniso_B[1][1] / _refine.aniso_B[1][3] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_all / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.ls_number_reflns_R_free / _refine.ls_number_reflns_R_work / _refine.ls_number_reflns_obs / _refine.ls_percent_reflns_R_free / _refine.ls_percent_reflns_obs / _refine.ls_wR_factor_R_free / _refine.ls_wR_factor_R_work / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.pdbx_average_fsc_free / _refine.pdbx_average_fsc_work / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_ligand / _refine_hist.pdbx_number_atoms_protein / _reflns.d_resolution_low / _reflns_shell.Rmerge_I_obs / _reflns_shell.meanI_over_sigI_obs / _reflns_shell.number_unique_obs / _reflns_shell.pdbx_CC_half / _reflns_shell.pdbx_Rpim_I_all / _reflns_shell.pdbx_redundancy / _struct.pdbx_CASP_flag / _struct_asym.entity_id / _struct_keywords.text / _struct_mon_prot_cis.pdbx_omega_angle / _struct_site.details / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site.pdbx_num_residues
Description: Ligand geometry / Details: geometry of heparan sulfate ligand corrected / Provider: author / Type: Coordinate replacement
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / 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 / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.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_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_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.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 3.1Jan 10, 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 3.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Heparanase
B: Heparanase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,7959
Polymers52,2762
Non-polymers1,5197
Water4,378243
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10800 Å2
ΔGint-39 kcal/mol
Surface area19030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.790, 71.290, 77.920
Angle α, β, γ (deg.)90.000, 95.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 43733.324 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase
#2: Protein Heparanase / Endo-glucoronidase / Heparanase-1 / Hpa1


Mass: 8542.769 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HPSE, HEP, HPA, HPA1, HPR1, HPSE1, HSE1 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q9Y251, heparanase

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Sugars , 2 types, 4 molecules

#3: Polysaccharide beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D- ...beta-D-glucopyranuronic acid-(1-4)-2-deoxy-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-beta-D-glucopyranuronic acid


Type: oligosaccharide / Mass: 611.482 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpAb1-4DGlcpNSa1-4DGlcpAb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122A-1b_1-5][a2122h-1a_1-5_2*NSO/3=O/3=O]/1-2-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpA]{[(4+1)][a-D-GlcpNSO3]{[(4+1)][b-D-GlcpA]{}}}LINUCSPDB-CARE
#5: 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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

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Non-polymers , 4 types, 246 molecules

#4: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5NO3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1 M MES [5.5] 0.1 M MgCl2 17% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 23, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.63→38.45 Å / Num. obs: 61989 / % possible obs: 99.5 % / Redundancy: 4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.63→1.67 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.077 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 4543 / CC1/2: 0.465 / Rpim(I) all: 0.625

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5e8m

5e8m


Resolution: 1.63→38.45 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.963 / WRfactor Rfree: 0.222 / WRfactor Rwork: 0.179 / SU B: 2.135 / SU ML: 0.07 / Average fsc free: 0.906 / Average fsc work: 0.9146 / Cross valid method: THROUGHOUT / ESU R: 0.086 / ESU R Free: 0.089
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflectionSelection details
Rfree0.2063 3083 4.975 %from apo structure
Rwork0.1697 58885 --
all0.171 ---
obs-61968 99.454 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 35.312 Å2
Baniso -1Baniso -2Baniso -3
1-1.14 Å20 Å20.351 Å2
2---1.096 Å20 Å2
3----0.105 Å2
Refinement stepCycle: LAST / Resolution: 1.63→38.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3686 0 54 243 3983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0133838
X-RAY DIFFRACTIONr_bond_other_d0.0020.0173604
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.6775206
X-RAY DIFFRACTIONr_angle_other_deg1.4121.6048370
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6965459
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.90121.823181
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.77815648
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5091522
X-RAY DIFFRACTIONr_chiral_restr0.0840.2494
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024182
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02819
X-RAY DIFFRACTIONr_nbd_refined0.2350.2722
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.23264
X-RAY DIFFRACTIONr_nbtor_refined0.1740.21861
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21671
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2209
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2690.212
X-RAY DIFFRACTIONr_nbd_other0.3020.231
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2320.28
X-RAY DIFFRACTIONr_mcbond_it3.2033.3661839
X-RAY DIFFRACTIONr_mcbond_other3.1943.3641838
X-RAY DIFFRACTIONr_mcangle_it4.4355.0362297
X-RAY DIFFRACTIONr_mcangle_other4.4355.0382298
X-RAY DIFFRACTIONr_scbond_it4.3493.9871999
X-RAY DIFFRACTIONr_scbond_other4.3523.9841996
X-RAY DIFFRACTIONr_scangle_it6.4425.7562909
X-RAY DIFFRACTIONr_scangle_other6.4395.7552908
X-RAY DIFFRACTIONr_lrange_it8.241.0464226
X-RAY DIFFRACTIONr_lrange_other8.20540.9974217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.63-1.6720.2832150.34323X-RAY DIFFRACTION99.6268
1.672-1.7180.2881960.2824249X-RAY DIFFRACTION99.9325
1.718-1.7680.2922130.2574168X-RAY DIFFRACTION99.7723
1.768-1.8220.2812220.2424004X-RAY DIFFRACTION99.7639
1.822-1.8820.252080.2083849X-RAY DIFFRACTION99.8278
1.882-1.9480.2142000.1893745X-RAY DIFFRACTION99.8229
1.948-2.0210.2282030.1823637X-RAY DIFFRACTION99.844
2.021-2.1040.2251740.193509X-RAY DIFFRACTION99.6752
2.104-2.1970.221710.1743342X-RAY DIFFRACTION99.8579
2.197-2.3050.2341700.1753221X-RAY DIFFRACTION99.8234
2.305-2.4290.2191650.1633036X-RAY DIFFRACTION99.8752
2.429-2.5760.2161570.1612888X-RAY DIFFRACTION99.5749
2.576-2.7540.2211500.1662691X-RAY DIFFRACTION99.2663
2.754-2.9740.2371310.1682495X-RAY DIFFRACTION98.8333
2.974-3.2580.2041340.1692316X-RAY DIFFRACTION98.7903
3.258-3.6410.1961000.162088X-RAY DIFFRACTION98.6919
3.641-4.2030.1531020.1411853X-RAY DIFFRACTION98.3895
4.203-5.1440.145790.1291571X-RAY DIFFRACTION98.6842
5.144-7.2590.2570.1681222X-RAY DIFFRACTION97.6336
7.259-38.450.218360.169679X-RAY DIFFRACTION96.1021

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