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- PDB-5qcu: Crystal structure of BACE complex with BMC022 -

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Basic information

Entry
Database: PDB / ID: 5qcu
TitleCrystal structure of BACE complex with BMC022
ComponentsBeta-secretase 1
KeywordsHYDROLASE / Hydroloase / D3R / BACE / Ligand Docking
Function / homology
Function and homology information


memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition ...memapsin 2 / Golgi-associated vesicle lumen / signaling receptor ligand precursor processing / beta-aspartyl-peptidase activity / amyloid precursor protein catabolic process / amyloid-beta formation / membrane protein ectodomain proteolysis / cellular response to manganese ion / amyloid-beta metabolic process / prepulse inhibition / detection of mechanical stimulus involved in sensory perception of pain / protein serine/threonine kinase binding / cellular response to copper ion / presynaptic modulation of chemical synaptic transmission / hippocampal mossy fiber to CA3 synapse / multivesicular body / response to lead ion / trans-Golgi network / recycling endosome / protein processing / cellular response to amyloid-beta / positive regulation of neuron apoptotic process / synaptic vesicle / late endosome / peptidase activity / amyloid-beta binding / endopeptidase activity / amyloid fibril formation / aspartic-type endopeptidase activity / lysosome / early endosome / endosome membrane / endosome / membrane raft / Amyloid fiber formation / endoplasmic reticulum lumen / axon / neuronal cell body / dendrite / Golgi apparatus / enzyme binding / cell surface / proteolysis / membrane / plasma membrane
Similarity search - Function
Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site ...Beta-secretase BACE1 / Beta-secretase BACE / Memapsin-like / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-E51 / Beta-secretase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.951 Å
Model detailsStructures for D3R docking challenge
AuthorsRondeau, J.M. / Shao, C. / Yang, H. / Burley, S.K.
CitationJournal: J.Comput.Aided Mol.Des. / Year: 2020
Title: D3R grand challenge 4: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies.
Authors: Parks, C.D. / Gaieb, Z. / Chiu, M. / Yang, H. / Shao, C. / Walters, W.P. / Jansen, J.M. / McGaughey, G. / Lewis, R.A. / Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Burley, S.K. / Amaro, R.E. / Gilson, M.K.
History
DepositionDec 1, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.2Feb 10, 2021Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-secretase 1
B: Beta-secretase 1
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)135,8166
Polymers134,3323
Non-polymers1,4843
Water10,809600
1
A: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2722
Polymers44,7771
Non-polymers4951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2722
Polymers44,7771
Non-polymers4951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-secretase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,2722
Polymers44,7771
Non-polymers4951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.173, 102.482, 100.443
Angle α, β, γ (deg.)90.000, 103.670, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21(chain B and (resid -2 through 157 or resid 170 through 385))
31(chain C and (resid -2 through 157 or resid 170 through 385))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain AA-2 - 385
211(chain B and (resid -2 through 157 or resid 170 through 385))B-2 - 157
221(chain B and (resid -2 through 157 or resid 170 through 385))B170 - 385
311(chain C and (resid -2 through 157 or resid 170 through 385))C-2 - 157
321(chain C and (resid -2 through 157 or resid 170 through 385))C170 - 385

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Components

#1: Protein Beta-secretase 1 / Aspartyl protease 2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP ...Aspartyl protease 2 / Asp 2 / Beta-site amyloid precursor protein cleaving enzyme 1 / Beta-site APP cleaving enzyme 1 / Memapsin-2 / Membrane-associated aspartic protease 2


Mass: 44777.336 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: BACE1, BACE, KIAA1149 / Production host: Escherichia coli (E. coli) / References: UniProt: P56817, memapsin 2
#2: Chemical ChemComp-E51 / (2R,4S)-N-butyl-4-[(5S,8S,10R)-5,10-dimethyl-3,3,6-trioxo-3lambda~6~-thia-7-azabicyclo[11.3.1]heptadeca-1(17),13,15-trien-8-yl]-4-hydroxy-2-methylbutanamide


Mass: 494.687 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H42N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 600 / 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: 3.02 Å3/Da / Density % sol: 59.3 %
Crystal growTemperature: 292 K / Method: hanging drop
Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M UNBUFFERED AMMONIUM SULFATE AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH X 8.3MG/ML IN 10MM TRIS-HCL PH 7.4, ...Details: CRYSTALS WERE GROWN AT 19C BY VAPOUR DIFFUSION IN HANGING DROPS USING 1.0M UNBUFFERED AMMONIUM SULFATE AS PRECIPITANT. PROTEIN STOCK WAS BACE MUT46B BATCH X 8.3MG/ML IN 10MM TRIS-HCL PH 7.4, 25MM NACL, WITH A 4-FOLD EXCESS OF BMC022 ADDED FROM A 50MM STOCK SOLUTION IN DMSO (1.4% DMSO IN DROP). CRYO-PROTECTANT WAS 2.0M LI2SO4, 0.2M SUCROSE, 0.1M CITRATE PH 5.5.

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00003
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Nov 11, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.951→55.289 Å / Num. obs: 115047 / % possible obs: 99.09 % / Rmerge(I) obs: 0.059

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHENIX1.12_2829refinement
CNXrefinement
CNXphasing
SCALEPACKdata scaling
DENZOdate reduction
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.951→55.289 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 18.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1931 11513 10.01 %
Rwork0.167 103534 -
obs0.1696 115047 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 163.55 Å2 / Biso mean: 43.1026 Å2 / Biso min: 20.25 Å2
Refinement stepCycle: final / Resolution: 1.951→55.289 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8895 0 102 600 9597
Biso mean--33.53 42.57 -
Num. residues----1130
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0079234
X-RAY DIFFRACTIONf_angle_d0.93512559
X-RAY DIFFRACTIONf_chiral_restr0.0621367
X-RAY DIFFRACTIONf_plane_restr0.0061610
X-RAY DIFFRACTIONf_dihedral_angle_d14.5565390
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5397X-RAY DIFFRACTION11.587TORSIONAL
12B5397X-RAY DIFFRACTION11.587TORSIONAL
13C5397X-RAY DIFFRACTION11.587TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9511-1.97320.23653470.20093243359094
1.9732-1.99650.23013980.19523359375798
1.9965-2.02080.21343840.18283472385698
2.0208-2.04640.21843920.17853369376198
2.0464-2.07330.2243760.17823395377198
2.0733-2.10170.20613730.17283394376798
2.1017-2.13180.20393980.17273434383298
2.1318-2.16360.21143670.16863368373599
2.1636-2.19740.19183700.16453458382899
2.1974-2.23340.19964090.17183413382299
2.2334-2.27190.21143670.16283466383399
2.2719-2.31320.19243930.16923443383699
2.3132-2.35770.21173850.17163413379899
2.3577-2.40590.2113930.17963413380699
2.4059-2.45820.19874060.176534963902100
2.4582-2.51530.22093750.171834673842100
2.5153-2.57820.2063770.17434543831100
2.5782-2.6480.20193860.178734853871100
2.648-2.72590.23514250.193334523877100
2.7259-2.81390.22064060.196634603866100
2.8139-2.91440.23073470.196935143861100
2.9144-3.03110.24023750.195734943869100
3.0311-3.1690.2173840.193634753859100
3.169-3.33610.21493710.194135413912100
3.3361-3.54510.18193780.165335103888100
3.5451-3.81870.1763870.145934633850100
3.8187-4.20290.14753980.131735123910100
4.2029-4.81080.13643850.121535013886100
4.8108-6.05990.18174080.152934873895100
6.0599-55.31140.20133530.18573583393699
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.1047-0.12290.02180.3212-0.19380.174-0.2374-0.1680.23850.18650.025-0.142-0.29580.1068-0.00440.3633-0.0419-0.07470.2819-0.00780.331343.598310.386925.1485
20.8745-0.15320.1240.8473-0.52390.8014-0.1340.18710.2632-0.08520.0299-0.0618-0.14320.0842-0.00010.3562-0.0705-0.04140.30050.05590.287442.314612.851412.0263
30.2634-0.04720.2240.3533-0.18180.2319-0.01350.02880.04230.2421-0.0335-0.1679-0.03110.02380.00010.3033-0.0253-0.02010.2701-0.01080.212744.0835-4.858126.8247
40.4159-0.178-0.1610.8001-0.18470.908-0.10370.2710.0909-0.09720.22110.293-0.0886-0.23830.0130.25670.0108-0.00520.30070.04880.309520.5332-6.813120.1896
50.31140.15470.13040.3574-0.30230.4602-0.0635-0.0056-0.05550.15970.10250.1704-0.0137-0.0286-0.00010.2875-00.04780.2457-0.00160.247924.7327-9.176429.7383
60.3780.1611-0.18330.0765-0.04540.3696-0.09950.15640.3260.10610.14040.1683-0.223-0.0381-0.00160.37630.0640.02490.29090.01950.411121.86623.523627.5896
70.3396-0.15570.18070.8381-0.54340.38-0.00710.03120.01670.01440.05780.1297-0.0544-0.0936-0.00010.3069-0.00550.03320.2765-0.01830.227133.9037-12.852524.7811
80.24710.162-0.07710.9607-0.01290.0480.3391-0.5734-0.28290.3058-0.2787-0.15520.0836-0.32460.02150.3306-0.0645-0.03240.44480.07840.28518.947511.0746-1.4569
90.1618-0.0830.01580.20680.11330.120.1006-0.1832-0.205-0.0011-0.11080.15190.1005-0.4412-00.2734-0.0841-0.00850.50970.08580.34488.05087.5208-7.105
100.58630.19540.05740.3605-0.1510.32480.1229-0.3401-0.33190.1258-0.13310.16990.192-0.60020.00130.234-0.0064-0.00690.5524-0.02660.32515.564112.1818-9.6507
110.88860.3919-0.3690.25730.11140.76320.1101-0.2307-0.00310.1046-0.14010.0247-0.158-0.23190.00010.27010.0381-0.03430.32680.03020.262919.191619.4468-10.4547
120.820.4989-0.11030.4121-0.14830.6467-0.11140.1825-0.4452-0.04480.0978-0.0415-0.01240.0252-0.0010.24620.0209-0.01680.3166-0.04820.303330.76713.9659-25.7094
130.8576-0.0692-0.310.6417-0.11490.1578-0.11850.3811-0.7505-0.2592-0.0043-0.01080.39980.0422-0.07420.46530.0160.10270.2753-0.19390.818732.7589-6.9563-26.2955
140.541-0.26440.03330.7044-0.2661.3505-0.06890.2388-0.698-0.088-0.1092-0.29740.19440.4115-0.36690.20910.16430.02350.0899-0.03440.702635.22260.7854-18.3973
150.33140.0284-0.22360.03450.01750.23280.09030.0595-0.26980.0157-0.0699-0.1418-0.0851-0.155300.25970.0031-0.05130.23520.00930.338527.954314.1511-17.0981
160.67110.1838-0.1930.32570.08470.17840.0150.0857-0.4094-0.0270.027-0.09030.00220.0991-0.00270.25860.028-0.04490.29880.04520.389737.685114.1402-20.7631
170.1467-0.1431-0.07340.12530.06360.37680.00920.1215-0.02760.0056-0.07460.30590.1386-0.3968-0.00010.2822-0.0350.00840.37260.0140.3887-1.5138-48.497837.3691
180.0951-0.06360.07940.17920.07360.15360.0036-0.2982-0.03560.1778-0.12660.0570.1624-0.0076-00.315-0.06280.06840.30490.0240.3043-1.698-51.815350.1863
190.55840.0705-0.55320.2729-0.1040.813-0.0265-0.1865-0.0940.1729-0.09030.14390.3406-0.2991-0.00410.3632-0.03690.02610.25270.05150.2972.568-55.598748.8602
200.17820.13010.05140.1606-0.09170.1796-0.0566-0.1416-0.27610.0849-0.0164-0.12520.51440.12750.00010.3450.03340.00640.2360.04910.336513.082-56.312139.9234
210.13430.1148-0.01850.0886-0.02990.02910.02060.0888-0.0266-0.127-0.01170.15780.0393-0.2789-0.00030.29220.029-0.05220.30660.00070.30844.4792-42.396529.4855
220.4960.0193-0.27360.7561-0.23780.31840.1251-0.08320.00850.111-0.0848-0.0727-0.10960.0998-0.00010.28910.0078-0.00960.30220.03710.288521.6803-35.059738.3652
230.89510.0429-0.30441.11260.28110.20020.2422-0.18140.15930.58710.05510.1756-0.5541-0.10210.13310.54290.03410.18180.3415-0.00190.365910.0876-19.131447.5319
240.32980.16330.15840.4042-0.29480.592-0.01270.0941-0.03010.09670.07240.2322-0.1392-0.12750.0030.30280.06760.08070.28230.0480.371911.0093-25.832636.7534
250.20080.3281-0.28330.6411-0.53610.51770.0907-0.0573-0.05520.2025-0.05010.09510.0316-0.08220.0020.25380.0580.0350.25120.00470.248411.8041-34.798739.5672
260.28810.2209-0.30020.4885-0.01540.44120.093-0.10520.12820.0952-0.0048-0.0125-0.10060.0975-00.29180.03840.01080.30130.02080.301618.951-31.814531.3413
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -2 through 32 )A-2 - 32
2X-RAY DIFFRACTION2chain 'A' and (resid 33 through 143 )A33 - 143
3X-RAY DIFFRACTION3chain 'A' and (resid 144 through 192 )A144 - 192
4X-RAY DIFFRACTION4chain 'A' and (resid 193 through 270 )A193 - 270
5X-RAY DIFFRACTION5chain 'A' and (resid 271 through 309 )A271 - 309
6X-RAY DIFFRACTION6chain 'A' and (resid 310 through 340 )A310 - 340
7X-RAY DIFFRACTION7chain 'A' and (resid 341 through 385 )A341 - 385
8X-RAY DIFFRACTION8chain 'B' and (resid -2 through 24 )B-2 - 24
9X-RAY DIFFRACTION9chain 'B' and (resid 25 through 53 )B25 - 53
10X-RAY DIFFRACTION10chain 'B' and (resid 54 through 116 )B54 - 116
11X-RAY DIFFRACTION11chain 'B' and (resid 117 through 183 )B117 - 183
12X-RAY DIFFRACTION12chain 'B' and (resid 184 through 233 )B184 - 233
13X-RAY DIFFRACTION13chain 'B' and (resid 234 through 271 )B234 - 271
14X-RAY DIFFRACTION14chain 'B' and (resid 272 through 327 )B272 - 327
15X-RAY DIFFRACTION15chain 'B' and (resid 328 through 349 )B328 - 349
16X-RAY DIFFRACTION16chain 'B' and (resid 350 through 385 )B350 - 385
17X-RAY DIFFRACTION17chain 'C' and (resid -2 through 32 )C-2 - 32
18X-RAY DIFFRACTION18chain 'C' and (resid 33 through 53 )C33 - 53
19X-RAY DIFFRACTION19chain 'C' and (resid 54 through 116 )C54 - 116
20X-RAY DIFFRACTION20chain 'C' and (resid 117 through 149 )C117 - 149
21X-RAY DIFFRACTION21chain 'C' and (resid 150 through 183 )C150 - 183
22X-RAY DIFFRACTION22chain 'C' and (resid 184 through 233 )C184 - 233
23X-RAY DIFFRACTION23chain 'C' and (resid 234 through 276 )C234 - 276
24X-RAY DIFFRACTION24chain 'C' and (resid 277 through 317 )C277 - 317
25X-RAY DIFFRACTION25chain 'C' and (resid 318 through 349 )C318 - 349
26X-RAY DIFFRACTION26chain 'C' and (resid 350 through 385 )C350 - 385

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