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- PDB-7aq1: Crystal structure of human mature meprin beta in complex with the... -

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Basic information

Entry
Database: PDB / ID: 7aq1
TitleCrystal structure of human mature meprin beta in complex with the specific inhibitor MWT-S-270
ComponentsMeprin B subunit beta
KeywordsHYDROLASE / Astacin protease / Metalloproteinase / Zn dependent / Sheddase / gamma Secretase / Inhbibitor bound Meprin beta holoenzyme / intermolecular disulfide bridge Homodimer / Glycoprotein
Function / homology
Function and homology information


meprin B / meprin A complex / metalloendopeptidase activity / inflammatory response / proteolysis / zinc ion binding / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Meprin alpha/beta subunit / Meprin peptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / : / TRAF/meprin, MATH domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MATH/TRAF domain ...Meprin alpha/beta subunit / Meprin peptidase domain / Astacin-like domain profile. / Peptidase M12A / Astacin (Peptidase family M12A) / : / TRAF/meprin, MATH domain / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MATH/TRAF domain / MATH/TRAF domain profile. / meprin and TRAF homology / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / TRAF-like / Peptidase, metallopeptidase / Zinc-dependent metalloprotease / Metallopeptidase, catalytic domain superfamily / EGF-like domain profile. / EGF-like domain / Neutral zinc metallopeptidases, zinc-binding region signature. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-RUE / Meprin A subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.413 Å
AuthorsLinnert, M. / Parthier, C. / Fritz, C.
Citation
Journal: Int J Mol Sci / Year: 2021
Title: Structure and Dynamics of Meprin beta in Complex with a Hydroxamate-Based Inhibitor.
Authors: Linnert, M. / Fritz, C. / Jager, C. / Schlenzig, D. / Ramsbeck, D. / Kleinschmidt, M. / Wermann, M. / Demuth, H.U. / Parthier, C. / Schilling, S.
#1: Journal: Preprints / Year: 2021
Title: Structure and Dynamics of Meprin beta in Complex with a Hydroxamate-Based Inhibitor
Authors: Linnert, M. / Fritz, C. / Jager, C. / Schlenzig, D. / Ramsbeck, D. / Kleinschmidt, M. / Wermann, M. / Demuth, H.-U. / Schilling, S.
History
DepositionOct 20, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 3, 2021Provider: repository / Type: Initial release
Revision 1.1Jun 16, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entity_branch_descriptor / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _citation.country / _citation.journal_id_ISSN ..._citation.country / _citation.journal_id_ISSN / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Meprin B subunit beta
B: Meprin B subunit beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)127,87726
Polymers121,5772
Non-polymers6,30124
Water7,512417
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, native gel electrophoresis, mass spectrometry
  • dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9390 Å2
ΔGint88 kcal/mol
Surface area45060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.250, 72.440, 135.470
Angle α, β, γ (deg.)90.000, 118.430, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-883-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))
21(chain B and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASNASNASPASP(chain A and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))AA62 - 3651 - 304
12VALVALALAALA(chain A and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))AA367 - 468306 - 407
13VALVALTHRTHR(chain A and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))AA470 - 594409 - 533
21ASNASNASPASP(chain B and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))BB62 - 3651 - 304
22VALVALALAALA(chain B and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))BB367 - 468306 - 407
23VALVALTHRTHR(chain B and (resid 62 through 365 or resid 367 through 468 or resid 470 through 594))BB470 - 594409 - 533

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Meprin B subunit beta / Endopeptidase-2 / Meprin B / N-benzoyl-L-tyrosyl-P-amino-benzoic acid hydrolase subunit beta / PABA ...Endopeptidase-2 / Meprin B / N-benzoyl-L-tyrosyl-P-amino-benzoic acid hydrolase subunit beta / PABA peptide hydrolase / PPH beta


Mass: 60788.398 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: following expression the promeprin beta was activated by trypsin due removal of the propeptide.
Source: (gene. exp.) Homo sapiens (human) / Gene: MEP1B / Production host: Komagataella pastoris (fungus) / Strain (production host): X33 / References: UniProt: Q16820, meprin B

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Sugars , 4 types, 9 molecules

#2: 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.: 2
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
#3: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_h2-i1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(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: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1_g2-h1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#10: 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.: 5 / Source method: obtained synthetically / 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 , 6 types, 432 molecules

#5: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#7: Chemical ChemComp-RUE / 3-[[(3-Carboxyphenyl)methyl-[2-(hydroxyamino)-2-oxoethyl]amino]methyl]benzoic acid / 3-[[(3-carboxyphenyl)methyl-[2-(oxidanylamino)-2-oxidanylidene-ethyl]amino]methyl]benzoic acid / MWT-S-270 / CHEMBL4216076


Mass: 358.345 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H18N2O6 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#9: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 417 / 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: 2.92 Å3/Da / Density % sol: 57.9 %
Crystal growTemperature: 286 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: Protein was mixed with inhibitor in a molar ratio of 1 to 1.2 to a final protein concentration of 8 mg/mL in 30 mM Tris, 100 mM sodium chloride, pH 7.6. 200 nL protein/inhibitor was mixed ...Details: Protein was mixed with inhibitor in a molar ratio of 1 to 1.2 to a final protein concentration of 8 mg/mL in 30 mM Tris, 100 mM sodium chloride, pH 7.6. 200 nL protein/inhibitor was mixed with 200 nL praezipitation buffer and equilibrated against 55 micro Liter of praezipitation buffer, containing 25 percent (w/v) PEG 4000 and 30 percent (v/v) ethylene glycol.

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1,5418
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
254181
ReflectionResolution: 2.41→44.969 Å / Num. obs: 103582 / % possible obs: 99.1 % / Redundancy: 5.64 % / Biso Wilson estimate: 49.027 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.119 / Rrim(I) all: 0.131 / Χ2: 1.041 / Net I/σ(I): 11.48 / Num. measured all: 584209 / Scaling rejects: 688
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.41-2.485.3181.0191.7939040768773410.7461.12995.5
2.48-2.545.6010.842.3742144754775250.8070.92899.7
2.54-2.625.6060.7582.6341451742773940.80.83899.6
2.62-2.75.6340.6313.0439847708970730.8650.69799.8
2.7-2.795.6680.5313.638908688468650.8820.58799.7
2.79-2.885.6820.4114.4237561664266100.9410.45499.5
2.88-2.995.6940.3245.4536446642164010.9530.35899.7
2.99-3.125.7230.246.8434999613461150.9750.26599.7
3.12-3.255.7350.1769.1734476603060110.9840.19499.7
3.25-3.415.730.14511.1832560571356820.9890.15999.5
3.41-3.65.730.10614.7930713538453600.9940.11799.6
3.6-3.825.6760.08517.9828893511650900.9960.09399.5
3.82-4.085.6860.07120.6826719475746990.9970.07998.8
4.08-4.415.5840.05724.9424384445243670.9980.06398.1
4.41-4.835.6190.05227.3623154419041210.9980.05898.4
4.83-5.45.6730.05526.3120422362936000.9980.0699.2
5.4-6.235.7180.05725.4218888332733030.9970.06399.3
6.23-7.635.690.05128.4315602275927420.9980.05699.4
7.63-10.795.5840.0435.0611989215821470.9980.04599.5
10.79-44.9695.2930.03940.686013117711360.9970.04496.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIXv1.14-3260refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gwn

4gwn


Resolution: 2.413→44.969 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 26.41 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.236 5193 5.02 %
Rwork0.1985 98304 -
obs0.2004 103497 99.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.96 Å2 / Biso mean: 55.5223 Å2 / Biso min: 25.32 Å2
Refinement stepCycle: final / Resolution: 2.413→44.969 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8542 0 791 417 9750
Biso mean--76.04 45.31 -
Num. residues----1066
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5114X-RAY DIFFRACTION6.635TORSIONAL
12B5114X-RAY DIFFRACTION6.635TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4131-2.44050.31831650.2987296890
2.4405-2.46930.35641760.28643299100
2.4693-2.49940.33721730.27043257100
2.4994-2.5310.32321750.2683315100
2.531-2.56430.30321720.28093286100
2.5643-2.59940.30971710.27463310100
2.5994-2.63660.33961670.27533220100
2.6366-2.67590.32481730.2523350100
2.6759-2.71770.33071720.25623288100
2.7177-2.76230.3341750.24963299100
2.7623-2.80990.26351750.23863313100
2.8099-2.8610.25911800.23923358100
2.861-2.9160.25171680.22433197100
2.916-2.97550.30141730.21943312100
2.9755-3.04020.26711710.22743279100
3.0402-3.11090.26221760.22783293100
3.1109-3.18870.26391730.233306100
3.1887-3.27490.26281750.21793316100
3.2749-3.37120.311770.21653281100
3.3712-3.480.22711730.20783312100
3.48-3.60430.24111760.23283100
3.6043-3.74850.24041740.18573284100
3.7485-3.91910.19071700.1783326799
3.9191-4.12550.22751710.1666325199
4.1255-4.38380.18141760.1437331498
4.3838-4.7220.15951690.1369322199
4.722-5.19650.18741780.1424329699
5.1965-5.9470.17031660.16753275100
5.947-7.4870.1791760.18783290100
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)
10.5754-0.0819-0.05770.2468-0.3030.68290.01890.1492-0.2219-0.05330.0177-0.01170.20370.1619-00.3719-0.00830.02570.4313-0.02160.29947.654432.9819.2632
20.16480.21930.13780.52230.27960.5333-0.10230.2415-0.0151-0.08230.14060.0336-0.04520.198900.3787-0.0895-0.00510.49960.0430.3076-2.310448.669212.7756
30.782-0.09410.30111.157-0.10491.30310.0274-0.1965-0.06210.3050.023-0.01160.038-0.162400.3772-0.0542-0.00570.34250.03980.3195-10.991335.081951.5343
40.67650.21140.26790.41750.14061.1138-0.03660.0317-0.0177-0.04240.04070.0068-0.07180.188900.3316-0.03520.01970.31330.0150.267810.85648.77241.2808
51.1944-0.01740.02370.1925-0.27580.38750.0133-0.0069-0.3987-0.0630.0397-0.10630.1973-0.15820.00020.4301-0.12450.01020.31580.01030.4674-29.678314.228726.7891
60.8169-0.04840.51940.0432-0.04310.32880.1525-0.6074-0.07850.00480.00870.12460.2055-0.23920.00020.417-0.0918-0.02290.49720.07030.4729-28.218520.790139.8728
70.51530.32170.22050.40330.00420.5162-0.0997-0.0050.263-0.14310.00480.2361-0.2386-0.1445-00.3793-0.0267-0.04310.35710.00940.476-24.572852.510818.5646
80.94280.37760.17450.6364-0.13470.6546-0.13150.07940.2027-0.08530.03570.26630.0224-0.2662-0.00010.3434-0.034-0.02820.5061-0.00220.4592-42.824138.19817.4
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 62 through 168 )A62 - 168
2X-RAY DIFFRACTION2chain 'A' and (resid 169 through 252 )A169 - 252
3X-RAY DIFFRACTION3chain 'A' and (resid 253 through 413 )A253 - 413
4X-RAY DIFFRACTION4chain 'A' and (resid 414 through 594 )A414 - 594
5X-RAY DIFFRACTION5chain 'B' and (resid 62 through 184 )B62 - 184
6X-RAY DIFFRACTION6chain 'B' and (resid 185 through 252 )B185 - 252
7X-RAY DIFFRACTION7chain 'B' and (resid 253 through 328 )B253 - 328
8X-RAY DIFFRACTION8chain 'B' and (resid 329 through 594 )B329 - 594

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  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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