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- PDB-6saz: Cleaved human fetuin-b in complex with crayfish astacin -

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Basic information

Entry
Database: PDB / ID: 6saz
TitleCleaved human fetuin-b in complex with crayfish astacin
Components
  • Astacin
  • Fetuin-B
KeywordsHYDROLASE / mammalian fertilization / sperm-egg fusion / polyspermy / metallopeptidase / protein inhibitor / limited proteolysis
Function / homology
Function and homology information


astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / metalloendopeptidase inhibitor activity / positive regulation of protein processing / negative regulation of endopeptidase activity / binding of sperm to zona pellucida ...astacin / glutamic-type peptidase activity / negative regulation of binding of sperm to zona pellucida / aspartic-type peptidase activity / prevention of polyspermy / cortical granule / metalloendopeptidase inhibitor activity / positive regulation of protein processing / negative regulation of endopeptidase activity / binding of sperm to zona pellucida / fertilization / cysteine-type endopeptidase inhibitor activity / endopeptidase inhibitor activity / single fertilization / metalloendopeptidase activity / peptidase activity / cell adhesion / proteolysis / extracellular exosome / zinc ion binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
Proteinase inhibitor I25C, fetuin, conserved site / Fetuin-B-type cystatin domain / Fetuin family signature 1. / Fetuin family signature 2. / Fetuin-B-type cystatin domain profile. / Astacin-like metallopeptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Cystatin domain ...Proteinase inhibitor I25C, fetuin, conserved site / Fetuin-B-type cystatin domain / Fetuin family signature 1. / Fetuin family signature 2. / Fetuin-B-type cystatin domain profile. / Astacin-like metallopeptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Collagenase (Catalytic Domain) / Collagenase (Catalytic Domain) / Metallopeptidase, catalytic domain superfamily / Neutral zinc metallopeptidases, zinc-binding region signature. / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Astacus astacus (noble crayfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsGomis-Ruth, F.X. / Guevara, T. / Cuppari, A. / Korschgen, H. / Schmitz, C. / Kuske, M. / Yiallouros, I. / Floehr, J. / Jahnen-Dechent, W. / Stocker, W.
Citation
Journal: Sci Rep / Year: 2019
Title: The C-terminal region of human plasma fetuin-B is dispensable for the raised-elephant-trunk mechanism of inhibition of astacin metallopeptidases.
Authors: Guevara, T. / Korschgen, H. / Cuppari, A. / Schmitz, C. / Kuske, M. / Yiallouros, I. / Floehr, J. / Jahnen-Dechent, W. / Stocker, W. / Gomis-Ruth, F.X.
#1: Journal: IUCrJ / Year: 2019
Title: Structure of mammalian plasma fetuin-B and its mechanism of selective metallopeptidase inhibition.
Authors: Cuppari, A. / Korschgen, H. / Fahrenkamp, D. / Schmitz, C. / Guevara, T. / Karmilin, K. / Kuske, M. / Olf, M. / Dietzel, E. / Yiallouros, I. / de Sanctis, D. / Goulas, T. / Weiskirchen, R. / ...Authors: Cuppari, A. / Korschgen, H. / Fahrenkamp, D. / Schmitz, C. / Guevara, T. / Karmilin, K. / Kuske, M. / Olf, M. / Dietzel, E. / Yiallouros, I. / de Sanctis, D. / Goulas, T. / Weiskirchen, R. / Jahnen-Dechent, W. / Floehr, J. / Stoecker, W. / Jovine, L. / Gomis-Ruth, F.X.
History
DepositionJul 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 2.0Jul 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 / struct_asym / struct_conn / struct_conn_type / 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.pdbx_formal_charge / _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 / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 24, 2024Group: 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: Astacin
B: Fetuin-B
C: Astacin
D: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,26410
Polymers130,0224
Non-polymers2,2426
Water55831
1
A: Astacin
B: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2345
Polymers65,0112
Non-polymers1,2223
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3760 Å2
ΔGint-44 kcal/mol
Surface area21430 Å2
MethodPISA
2
C: Astacin
D: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0305
Polymers65,0112
Non-polymers1,0193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-47 kcal/mol
Surface area20620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.700, 90.700, 283.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Astacin / / Crayfish small molecule proteinase


Mass: 22913.318 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Astacus astacus (noble crayfish) / References: UniProt: P07584, astacin
#2: Protein Fetuin-B / 16G2 / Fetuin-like protein IRL685 / Gugu


Mass: 42097.820 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence stretches MGLLLPLALCILVLCCGAMSPPQL, CTKSQASSCSLQS, SQAPATGSENSAVNQKPTNLPKVEESQQKNTPPTDSPSKAGPRGSVQYLPDLDDKNSQEKGPQEAFPVHLDLTTNPQGETLDISFLFLEPMEEKLVVLPFPKEKA, and PLVLPP missing from coordinate file.
Source: (gene. exp.) Homo sapiens (human) / Gene: FETUB / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q9UGM5

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Sugars , 3 types, 4 molecules

#3: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#6: 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.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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 , 2 types, 33 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 3.46 Å3/Da / Density % sol: 64.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan ...Details: Crystallization assays were set up following the sitting-drop vapor diffusion method at the joint IBMB/IRB Automated Crystallography Platform of Barcelona Science Park. A Tecan robot (Tecan Trading) was used to prepare reservoir solutions, and a Cartesian Microsys 4000 XL robot (Genomic Solutions) or a Phoenix nanodrop robot (Art Robbins Instruments) dispensed nanocrystallization drops on 96x2-well Swissci Polystyrene MRC Crystallization Plates (Molecular Dimensions). Plates were stored at 4 or 20 degrees in thermostatic crystal farms (Bruker AXS). The astacin-hFB complex only crystallized after incubating the inhibitor (at 7.5 mg/mL) with six-fold molar excess of the peptidase in 10 mM Tris-HCl, 140 mM sodium chloride, pH 6.8. Crystals were obtained at 20 degrees in 200 nL:100 nL drops with protein complex solution and 20 percent (w/v) polyethylene glycol 3,350, 0.2 M sodium tartrate dibasic as reservoir solution.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 1.0032 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 11, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0032 Å / Relative weight: 1
ReflectionResolution: 3→78.5 Å / Num. obs: 26287 / % possible obs: 99.7 % / Redundancy: 9.2 % / Biso Wilson estimate: 70.5 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.184 / Rrim(I) all: 0.195 / Net I/σ(I): 11.1
Reflection shellResolution: 3→3.18 Å / Redundancy: 8.9 % / Rmerge(I) obs: 1.565 / Num. unique obs: 4165 / CC1/2: 0.626 / Rrim(I) all: 1.66 / % possible all: 98.9

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Processing

Software
NameClassification
BUSTER-TNTrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6HT9

6ht9


Resolution: 3→78.5 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflectionSelection details
Rfree0.247 708 -Random
Rwork0.185 ---
obs-25577 99.7 %-
Displacement parametersBiso mean: 82.4 Å2
Refinement stepCycle: LAST / Resolution: 3→78.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6832 0 142 31 7005

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