Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  BACE2 XAPERONE COMPLEX
 
Authors :  D. W. Banner, A. Kuglstatter, J. Benz, M. Stihle, A. Ruf
Date :  24 Jan 13  (Deposition) - 29 May 13  (Release) - 03 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.51
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Hydrolase-Immune System Complex, Nanobody (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. W. Banner, B. Gsell, J. Benz, J. Bertschinger, D. Burger, S. Brack, S. Cuppuleri, M. Debulpaep, A. Gast, D. Grabulovski, M. Hennig, H. Hilpert, W. Huber, A. Kuglstatter, E. Kusznir, T. Laeremans, H. Matile, C. Miscenic, A. Rufer, D. Schlatter, J. Steyeart, M. Stihle R. Thoma, M. Weber, A. Ruf
Mapping The Conformational Space Accessible To Bace2 Using Surface Mutants And Co-Crystals With Fab-Fragments, Fynomers, And Xaperones
Acta Crystallogr. , Sect. D V. 69 1124 2013
PubMed-ID: 23695257  |  Reference-DOI: 10.1107/S0907444913006574

(-) Compounds

Molecule 1 - BETA-SECRETASE 2
    ChainsA
    EC Number3.4.23.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentEXTRACELLULAR, RESIDUES 75-460
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASPARTIC-LIKE PROTEASE 56 KDA, ASPARTYL PROTEASE 1, ASP1, ASP 1, BETA-SITE AMYLOID PRECURSOR PROTEIN CLEAVING ENZYME 2, BETA-SITE APP CLEAVING ENZYME 2, DOWN REGION ASPARTIC PROTEASE, DRAP, MEMAPSIN-1, MEMBRANE-ASSOCIATED ASPARTIC PROTEASE 1, THETA-SECRETASE, BACE2
 
Molecule 2 - XA4813
    ChainsD
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMESY4
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonLLAMA
    Organism ScientificLAMA GLAMA
    Organism Taxid9844

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1B3P1Ligand/Ion2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2CL1Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:48 , TYR A:87 , PHE A:124 , TYR A:211 , ILE A:239 , ASP A:241 , GLY A:243 , THR A:244 , HOH A:2038 , HOH A:2040 , HOH A:2135 , HOH A:2227 , HOH A:2228 , HOH A:2296BINDING SITE FOR RESIDUE B3P A1399
2AC2SOFTWAREASN A:114 , SER A:148 , GLU A:150 , ILE D:192BINDING SITE FOR RESIDUE CL A1400

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:171 -A:371
2A:230 -A:395
3A:282 -A:331
4D:181 -D:255

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Thr A:38 -Pro A:39
2Lys A:144 -Pro A:145
3Gly A:384 -Pro A:385

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ZKQ)

(-) PROSITE Motifs  (2, 3)

Asymmetric/Biological Unit (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.BACE2_HUMAN92-429  1A:30-367
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.BACE2_HUMAN107-118
300-311
  2A:45-56
A:238-249

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000003303331ENSE00001304779chr21:42539728-42540502775BACE2_HUMAN1-1041041A:13-4230
1.3aENST000003303333aENSE00001294412chr21:42598193-4259828189BACE2_HUMAN105-134301A:43-7230
1.6ENST000003303336ENSE00001313528chr21:42609440-42609656217BACE2_HUMAN134-206731A:72-14473
1.7dENST000003303337dENSE00001293136chr21:42613746-42613874129BACE2_HUMAN207-249431A:145-187 (gaps)43
1.8ENST000003303338ENSE00001315110chr21:42615303-42615437135BACE2_HUMAN250-294451A:188-23245
1.9aENST000003303339aENSE00001299298chr21:42617889-42617990102BACE2_HUMAN295-328341A:233-26634
1.10ENST0000033033310ENSE00001319314chr21:42622679-42622828150BACE2_HUMAN329-378501A:267-31650
1.12ENST0000033033312ENSE00001297180chr21:42629085-42629253169BACE2_HUMAN379-435571A:317-373 (gaps)57
1.13cENST0000033033313cENSE00001820917chr21:42647298-426485241227BACE2_HUMAN435-518841A:373-39826

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:376
 aligned with BACE2_HUMAN | Q9Y5Z0 from UniProtKB/Swiss-Prot  Length:518

    Alignment length:386
                                    84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454      
          BACE2_HUMAN    75 ANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAGLPVAGSGTNGGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMMGAGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPA 460
               SCOP domains d3zkqa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..eeeehhheeeeeeee................................hhhhh...eeeeeeeeeee..eeeeeeeeeeeee....................................hhhhh.......hhhhhhhhhhh....eeeee....---------.eeeee...hhhhh....eeee..........eeeeee..ee...hhhhhh...eee......eeeehhhhhhhhhhhhhhh.....hhhhhh....eeee....hhhhh..eeeeee.....eeeeeeehhhhheeee.-....eeeeee.eeee...eeehhhhhh.eeeeee....eeeeee....ee..ee.eeeeeeee........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------PEPTIDASE_A1  PDB: A:30-367 UniProt: 92-429                                                                                                                                                                                                                                                                                                       ------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------ASP_PROTEASE-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:13-42        Exon 1.3a  PDB: A:43-72       ------------------------------------------------------------------------Exon 1.7d  PDB: A:145-187 (gaps)           Exon 1.8  PDB: A:188-232 UniProt: 250-294    Exon 1.9a  PDB: A:233-266         Exon 1.10  PDB: A:267-316 UniProt: 329-378        Exon 1.12  PDB: A:317-373 (gaps) UniProt: 379-435        ------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.6  PDB: A:72-144 UniProt: 134-206                                 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.13c  PDB: A:373-398 Transcript 1 (2)
                 3zkq A  13 ANFLAMVDNLQGDSGRGYYLEMLIGTPPQKLQILVDTGSSNFAVAGTPHSYIDTYFDTERSSTYRSKGFDVTVKYTQGSWTGFVGEDLVTIPKGFNTSFLVNIATIFESENFFLPGIKWNGILGLAYATLAKPSSSLETFFDSLVTQANIPNVFSMQMCGAG---------GGSLVLGGIEPSLYKGDIWYTPIKEEWYYQIEILKLEIGGQSLNLDCREYNADKAIVDSGTTLLRLPQKVFDAVVEAVARASLIPEFSDGFWTGSQLACWTNSETPWSYFPKISIYLRDENSSRSFRITILPQLYIQPMM-AGLNYECYRFGISPSTNALVIGATVMEGFYVIFDRAQKRVGFAASPCAEIAGAAVSEISGPFSTEDVASNCVPA 398
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172 |       - |     192       202       212       222       232       242       252       262       272       282       292       302       312       322| |    332       342       352       362       372       382       392      
                                                                                                                                                                                           174       184                                                                                                                                        323 |                                                                         
                                                                                                                                                                                                                                                                                                                                                  325                                                                         

Chain D from PDB  Type:PROTEIN  Length:113
                                                                                                                                                 
               SCOP domains d3zkqd_ D: automated matches                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeeehhh.eeeeee...hhhhheeeeeee..ee...eeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------- Transcript
                 3zkq D 161 VQLQESGGGLVQPGGSLRLSCAASGFTFSSAIMTWVRQAPGKGREWVSTIGSDGSITTYADSVKGRFTISRDNARNTLYLQMNSLKPEDTAVYYCTSAGRRGPGTQVTVSSHH 273
                                   170       180       190       200       210       220       230       240       250       260       270   

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZKQ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZKQ)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (BACE2_HUMAN | Q9Y5Z0)
molecular function
    GO:0001540    amyloid-beta binding    Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
    GO:0004190    aspartic-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0050435    amyloid-beta metabolic process    The chemical reactions and pathways involving amyloid-beta, a glycoprotein associated with Alzheimer's disease, and its precursor, amyloid precursor protein (APP).
    GO:0006509    membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
    GO:0042985    negative regulation of amyloid precursor protein biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of amyloid precursor protein (APP), the precursor of amyloid-beta.
    GO:0016486    peptide hormone processing    The generation of a mature peptide hormone by posttranslational processing of a prohormone.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005768    endosome    A vacuole to which materials ingested by endocytosis are delivered.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    B3P  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:384 - Pro A:385   [ RasMol ]  
    Lys A:144 - Pro A:145   [ RasMol ]  
    Thr A:38 - Pro A:39   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3zkq
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  BACE2_HUMAN | Q9Y5Z0
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.23.45
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  BACE2_HUMAN | Q9Y5Z0
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BACE2_HUMAN | Q9Y5Z02ewy 3zkg 3zki 3zkm 3zkn 3zks 3zkx 3zl7 3zlq 4bel 4bfb

(-) Related Entries Specified in the PDB File

3zkg BACE2 MUTANT APO STRUCTURE
3zki BACE2 MUTANT STRUCTURE WITH LIGAND
3zkm BACE2 FAB COMPLEX
3zkn BACE2 FAB INHIBITOR COMPLEX
3zks BACE2 XAPERONE COMPLEX WITH INHIBITOR
3zkx TERNARY BACE2 XAPERONE COMPLEX
3zl7 BACE2 FYNOMER COMPLEX
3zov CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH CHEMICAL LIGAND