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- PDB-6hpv: Crystal structure of mouse fetuin-B -

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Basic information

Entry
Database: PDB / ID: 6hpv
TitleCrystal structure of mouse fetuin-B
ComponentsFetuin-B
Keywordshydrolase inhibitor / Glycoprotein / cystatin domain / fertilization / egg coat / zona pellucida / hardening / metalloprotease inhibitor / ovastacin / ZP2 / liver-secreted protein
Function / homology
Function and homology information


metalloendopeptidase inhibitor activity / binding of sperm to zona pellucida / negative regulation of endopeptidase activity / cysteine-type endopeptidase inhibitor activity / single fertilization / extracellular space / extracellular region
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. / Cystatin domain / Cystatin-like domain / Cystatin domain / Cystatin superfamily
Similarity search - Domain/homology
ACETATE ION / Fetuin-B
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsFahrenkamp, D. / Dietzel, E. / de Sanctis, D. / Jovine, L.
Funding support Sweden, Germany, 3items
OrganizationGrant numberCountry
Swedish Research Council2016-03999 Sweden
European Molecular Biology Organization Germany
German Research Foundation
Citation
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.
#1: Journal: Biochem. J. / Year: 2000
Title: Fetuin-B, a second member of the fetuin family in mammals.
Authors: Olivier, E. / Soury, E. / Ruminy, P. / Husson, A. / Parmentier, F. / Daveau, M. / Salier, J.P.
#2: Journal: Biochem. J. / Year: 2003
Title: Tissue distribution and activity testing suggest a similar but not identical function of fetuin-B and fetuin-A.
Authors: Denecke, B. / Graber, S. / Schafer, C. / Heiss, A. / Woltje, M. / Jahnen-Dechent, W.
#3: Journal: Dev. Cell / Year: 2013
Title: Fetuin-B, a liver-derived plasma protein is essential for fertilization.
Authors: Dietzel, E. / Wessling, J. / Floehr, J. / Schafer, C. / Ensslen, S. / Denecke, B. / Rosing, B. / Neulen, J. / Veitinger, T. / Spehr, M. / Tropartz, T. / Tolba, R. / Renne, T. / Egert, A. / ...Authors: Dietzel, E. / Wessling, J. / Floehr, J. / Schafer, C. / Ensslen, S. / Denecke, B. / Rosing, B. / Neulen, J. / Veitinger, T. / Spehr, M. / Tropartz, T. / Tolba, R. / Renne, T. / Egert, A. / Schorle, H. / Gottenbusch, Y. / Hildebrand, A. / Yiallouros, I. / Stocker, W. / Weiskirchen, R. / Jahnen-Dechent, W.
#4: Journal: Biol. Chem. / Year: 2014
Title: Mammalian gamete fusion depends on the inhibition of ovastacin by fetuin-B.
Authors: Stocker, W. / Karmilin, K. / Hildebrand, A. / Westphal, H. / Yiallouros, I. / Weiskirchen, R. / Dietzel, E. / Floehr, J. / Jahnen-Dechent, W.
#5: Journal: Cell Metab. / Year: 2015
Title: Fetuin B Is a Secreted Hepatocyte Factor Linking Steatosis to Impaired Glucose Metabolism.
Authors: Meex, R.C. / Hoy, A.J. / Morris, A. / Brown, R.D. / Lo, J.C. / Burke, M. / Goode, R.J. / Kingwell, B.A. / Kraakman, M.J. / Febbraio, M.A. / Greve, J.W. / Rensen, S.S. / Molloy, M.P. / ...Authors: Meex, R.C. / Hoy, A.J. / Morris, A. / Brown, R.D. / Lo, J.C. / Burke, M. / Goode, R.J. / Kingwell, B.A. / Kraakman, M.J. / Febbraio, M.A. / Greve, J.W. / Rensen, S.S. / Molloy, M.P. / Lancaster, G.I. / Bruce, C.R. / Watt, M.J.
#6: Journal: Hum. Reprod. / Year: 2016
Title: Association of high fetuin-B concentrations in serum with fertilization rate in IVF: a cross-sectional pilot study.
Authors: Floehr, J. / Dietzel, E. / Neulen, J. / Rosing, B. / Weissenborn, U. / Jahnen-Dechent, W.
#7: Journal: Mol. Hum. Reprod. / Year: 2017
Title: Recombinant fetuin-B protein maintains high fertilization rate in cumulus cell-free mouse oocytes.
Authors: Dietzel, E. / Floehr, J. / Van de Leur, E. / Weiskirchen, R. / Jahnen-Dechent, W.
#8: Journal: Diabetes Metab. / Year: 2017
Title: The novel adipokine/hepatokine fetuin B in severe human and murine diabetic kidney disease.
Authors: Kralisch, S. / Hoffmann, A. / Kloting, N. / Bachmann, A. / Kratzsch, J. / Bluher, M. / Zhang, M.Z. / Harris, R.C. / Stumvoll, M. / Fasshauer, M. / Ebert, T.
#9: Journal: Dev. Biol. / Year: 2018
Title: Maternal malnourishment induced upregulation of fetuin-B blunts nephrogenesis in the low birth weight neonate.
Authors: Rabadi, M.M. / Abdulmahdi, W. / Nesi, L. / Jules, E. / Marghani, Y. / Sheinin, E. / Tilzer, J. / Gupta, S. / Chen, S. / Cassimatis, N.D. / Lipphardt, M. / Kozlowski, P.B. / Ratliff, B.B.
#10: Journal: Sci Rep / Year: 2019
Title: Mammalian plasma fetuin-B is a selective inhibitor of ovastacin and meprin metalloproteinases.
Authors: Karmilin, K. / Schmitz, C. / Kuske, M. / Korschgen, H. / Olf, M. / Meyer, K. / Hildebrand, A. / Felten, M. / Fridrich, S. / Yiallouros, I. / Becker-Pauly, C. / Weiskirchen, R. / Jahnen- ...Authors: Karmilin, K. / Schmitz, C. / Kuske, M. / Korschgen, H. / Olf, M. / Meyer, K. / Hildebrand, A. / Felten, M. / Fridrich, S. / Yiallouros, I. / Becker-Pauly, C. / Weiskirchen, R. / Jahnen-Dechent, W. / Floehr, J. / Stocker, W.
History
DepositionSep 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 20, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2019Group: Author supporting evidence / Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_audit_support / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fetuin-B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,4564
Polymers41,9541
Non-polymers5013
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area700 Å2
ΔGint6 kcal/mol
Surface area15780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.710, 67.710, 197.810
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-573-

HOH

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Components

#1: Protein Fetuin-B / Fetuin-like protein IRL685


Mass: 41954.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Fetub / Plasmid: pHLsec2 / Cell line (production host): HEK293S GnTI- / Production host: Homo sapiens (human) / References: UniProt: Q9QXC1
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
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
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.71 Å3/Da / Density % sol: 54.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 150 mM NaCl, 100 mM NaOAc, 20 mM Na-HEPES pH 7.8, 25% PEG 4000, 8% isopropanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.7712 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 28, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.7712 Å / Relative weight: 1
ReflectionResolution: 2.3→47.9 Å / Num. obs: 19993 / % possible obs: 93.6 % / Redundancy: 19.3 % / Biso Wilson estimate: 54.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.024 / Rrim(I) all: 0.112 / Net I/σ(I): 20.34
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 6 % / Rmerge(I) obs: 1.626 / Mean I/σ(I) obs: 1.36 / Num. unique obs: 1303 / CC1/2: 0.521 / Rpim(I) all: 0.71 / Rrim(I) all: 1.782 / % possible all: 63

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Processing

Software
NameVersionClassification
PHENIX1.14-3260refinement
XDSJan 26, 2018 BUILT=20180409data reduction
XSCALEJan 26, 2018 BUILT=20180409data scaling
CRANK22.0.166phasing
PHENIX1.13-2998model building
Coot0.8.9.1model building
RefinementMethod to determine structure: SAD / Resolution: 2.3→47.878 Å / SU ML: 0.34 / Cross valid method: FREE R-VALUE / σ(F): 1.41 / Phase error: 29.12 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2529 1000 5 %
Rwork0.2241 --
obs0.2255 19991 93.63 %
Solvent computationShrinkage radii: 0.8 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.3→47.878 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2338 0 32 85 2455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022435
X-RAY DIFFRACTIONf_angle_d0.5863316
X-RAY DIFFRACTIONf_dihedral_angle_d13.365942
X-RAY DIFFRACTIONf_chiral_restr0.043372
X-RAY DIFFRACTIONf_plane_restr0.006434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2999-2.42120.3561010.31321901X-RAY DIFFRACTION67
2.4212-2.57290.34571300.3052489X-RAY DIFFRACTION89
2.5729-2.77150.37121470.30142799X-RAY DIFFRACTION99
2.7715-3.05040.30451510.2742872X-RAY DIFFRACTION100
3.0504-3.49170.29071520.24822882X-RAY DIFFRACTION100
3.4917-4.39860.23421540.19352926X-RAY DIFFRACTION100
4.3986-47.88860.20231650.19333122X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.70160.5417-0.50460.1763-0.09112.0508-0.013-0.07170.05490.06240.04980.0242-0.1597-0.0953-00.43780.06630.010.4329-0.0040.46575.92823.179485.117
20.8807-0.6638-0.59870.61430.2330.82060.06930.43380.3802-0.18460.0361-0.20940.0003-0.15100.50140.01830.02580.5610.1770.584718.271538.626261.4045
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and resi 31:157 or resi 296:388 or resi 900:910
2X-RAY DIFFRACTION2chain A and resi 158:269

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