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- PDB-6yjy: Crystal structure of human glutaminyl cyclase in complex with neu... -

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Basic information

Entry
Database: PDB / ID: 6yjy
TitleCrystal structure of human glutaminyl cyclase in complex with neurotensin 1-5
ComponentsGlutaminyl-peptide cyclotransferase
KeywordsTRANSFERASE / ALPHA-BETA PROTEIN / METALLOPROTEIN / INTERMEDIATE
Function / homology
Function and homology information


peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase / glutaminyl-peptide cyclotransferase activity / protein modification process / specific granule lumen / tertiary granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / zinc ion binding / extracellular region
Similarity search - Function
M28 Zn-Peptidase Glutaminyl Cyclase / Glutaminyl-peptide cyclotransferase-like / Peptidase M28 / Peptidase family M28 / Zn peptidases / Aminopeptidase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
GLUTAMINE / LEUCINE / PYROGLUTAMIC ACID / TYROSINE / Glutaminyl-peptide cyclotransferase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsFunk, L.M. / Sautner, V. / Tittmann, K.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)IRTG 1422 Germany
CitationJournal: Biochemistry / Year: 2020
Title: Hydrazides Are Potent Transition-State Analogues for Glutaminyl Cyclase Implicated in the Pathogenesis of Alzheimer's Disease.
Authors: Kupski, O. / Funk, L.M. / Sautner, V. / Seifert, F. / Worbs, B. / Ramsbeck, D. / Meyer, F. / Diederichsen, U. / Buchholz, M. / Schilling, S. / Demuth, H.U. / Tittmann, K.
History
DepositionApr 5, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / struct_conn / struct_conn_type
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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_type.id
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Glutaminyl-peptide cyclotransferase
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,40731
Polymers75,1072
Non-polymers3,30129
Water8,665481
1
A: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,02414
Polymers37,5531
Non-polymers1,47113
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glutaminyl-peptide cyclotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,38317
Polymers37,5531
Non-polymers1,83016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)119.274, 119.274, 334.459
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-660-

HOH

21A-739-

HOH

31B-656-

HOH

41B-657-

HOH

51B-671-

HOH

61B-689-

HOH

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Glutaminyl-peptide cyclotransferase / / Glutaminyl cyclase / sQC / Glutaminyl-tRNA cyclotransferase / Glutamyl cyclase / EC


Mass: 37553.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: QPCT / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: Q16769, glutaminyl-peptide cyclotransferase

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Non-polymers , 8 types, 510 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-PCA / PYROGLUTAMIC ACID / Pyroglutamic acid


Type: L-peptide linking / Mass: 129.114 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C5H7NO3 / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LEU / LEUCINE / Leucine


Type: L-peptide linking / Mass: 131.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO2 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TYR / TYROSINE / Tyrosine


Type: L-peptide linking / Mass: 181.189 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C9H11NO3 / Feature type: SUBJECT OF INVESTIGATION
#8: Chemical ChemComp-GLN / GLUTAMINE / Glutamine


Type: L-peptide linking / Mass: 146.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H10N2O3 / Feature type: SUBJECT OF INVESTIGATION
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 481 / 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: 3.05 Å3/Da / Density % sol: 59.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 1.6M ammonium sulfate, 0.1M MES pH 6.5, 4% (v/v) 1,4-Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.67→64.991 Å / Num. obs: 106183 / % possible obs: 99.9 % / Redundancy: 20.343 % / Biso Wilson estimate: 37.6 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.057 / Rrim(I) all: 0.058 / Χ2: 1.068 / Net I/σ(I): 30.62 / Num. measured all: 2160103 / Scaling rejects: 250
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.67-1.7719.743.1771.08168050.5523.2699.7
1.77-1.8720.8241.6042.27134530.8221.644100
1.87-220.6580.824.5137080.9370.84100
2-520.4540.04643.465802510.047100
5-1019.0230.016146.37363110.016100
10-2516.9040.015160.952010.01599
25-509.1110.02113.243610.02292.3
50-10020.01131.66510.01662.5

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.13_2998refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AFM

2afm


Resolution: 1.67→64.991 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.32
RfactorNum. reflection% reflection
Rfree0.1884 5275 4.97 %
Rwork0.1694 --
obs0.1704 106140 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 172.57 Å2 / Biso mean: 43.0046 Å2 / Biso min: 24.5 Å2
Refinement stepCycle: final / Resolution: 1.67→64.991 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5306 0 184 481 5971
Biso mean--76.57 47.06 -
Num. residues----658
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.67-1.68890.61671630.6141329699
1.6889-1.70880.53891730.5693356100
1.7088-1.72960.53371730.52173313100
1.7296-1.75150.48881590.43793345100
1.7515-1.77460.37531730.37023321100
1.7746-1.79890.38071760.33063344100
1.7989-1.82460.3111740.28893333100
1.8246-1.85180.26821750.2653314100
1.8518-1.88080.2561750.24373324100
1.8808-1.91160.27311760.22413343100
1.9116-1.94460.25621760.21293353100
1.9446-1.97990.24021760.20153338100
1.9799-2.0180.23651760.19683352100
2.018-2.05920.20251760.18483340100
2.0592-2.1040.19631760.17793335100
2.104-2.15290.19191760.17393355100
2.1529-2.20680.17461770.16613352100
2.2068-2.26640.18421760.16833347100
2.2664-2.33310.21011770.16413361100
2.3331-2.40850.1921760.15863351100
2.4085-2.49450.21371770.1683359100
2.4945-2.59440.19581780.1653378100
2.5944-2.71250.19961770.16123361100
2.7125-2.85550.20421780.16793395100
2.8555-3.03440.18371770.17063363100
3.0344-3.26870.19871780.16553382100
3.2687-3.59760.15381800.15653406100
3.5976-4.11810.15681800.13453432100
4.1181-5.18810.13651820.12683445100
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)
17.2387-1.23814.83653.08430.16817.21650.38740.3661-0.5177-0.192-0.00170.14060.69220.283-0.54690.2898-0.08730.0480.14740.02390.3006-18.5821-24.667915.0385
21.31-0.20230.09031.31420.23591.0305-0.0356-0.02960.08070.14950.02140.1539-0.0374-0.22010.02550.283-0.01230.02380.31050.0230.3156-28.915-2.809226.9156
34.16190.59-0.19126.3132-0.08153.7285-0.04840.0333-0.63430.17780.02920.02360.5536-0.3733-0.03980.2681-0.0970.01540.29640.00080.3196-30.128-20.273120.6944
40.6536-0.50870.30161.0749-0.39891.8904-0.032-0.0450.07490.15550.0363-0.0843-0.0610.0224-0.00860.2828-0.0285-0.00560.26570.00520.3211-16.2394-7.897127.9854
53.0377-1.53553.28672.5782-2.23717.75050.00820.24960.114-0.2272-0.0904-0.23410.18940.3860.0860.25880.00370.04850.28170.00050.2844-14.538-12.04675.5399
60.9021-0.210.33212.9801-0.27381.77980.01180.07280.0322-0.099-0.0187-0.0158-0.0304-0.00720.0280.2218-0.01950.03940.28650.00890.2657-18.9656-5.23816.2495
70.7659-0.41650.24082.0758-0.13311.262-0.015-0.0975-0.11290.17560.04590.2-0.1403-0.1578-0.01290.34750.00780.04530.28380.04750.3312-20.0005-18.799561.7601
84.08670.5306-0.91743.51462.01263.90160.061-0.20760.47650.1762-0.08750.8747-0.3432-0.83870.10380.41280.06930.14670.42030.08770.5433-32.1265-13.949266.228
91.0019-0.6550.05132.0113-0.32481.572-0.0859-0.22140.08420.47660.097-0.0797-0.38720.0171-0.02310.46120.00820.0120.2755-0.00240.2687-14.5669-10.144768.0644
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 33 through 59 )A33 - 59
2X-RAY DIFFRACTION2chain 'A' and (resid 60 through 160 )A60 - 160
3X-RAY DIFFRACTION3chain 'A' and (resid 161 through 190 )A161 - 190
4X-RAY DIFFRACTION4chain 'A' and (resid 191 through 261 )A191 - 261
5X-RAY DIFFRACTION5chain 'A' and (resid 262 through 300 )A262 - 300
6X-RAY DIFFRACTION6chain 'A' and (resid 301 through 361 )A301 - 361
7X-RAY DIFFRACTION7chain 'B' and (resid 33 through 160 )B33 - 160
8X-RAY DIFFRACTION8chain 'B' and (resid 161 through 190 )B161 - 190
9X-RAY DIFFRACTION9chain 'B' and (resid 191 through 361 )B191 - 361

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