How to search the PDB

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1 Hw t search the PDB us: The searchbx n the PDBe hmepage allws yu t switch between searching and dwnlading data frm the PDB and the EMDB archive The search bx n the PDBe website prvides an autcmplete feature, which displays suggested search terms. These are categrised by cntext, e.g. authr, mlecule name, species etc. 1 P a g e

2 Search results are rganised in a way that highlights different features f the search. They are srted by unique macrmlecules, type f macrmlecules, interacting macrmlecules, experimental methds, assembly cmpsitin, species names etc. The best representative structure frm a particular prtein family is always the tp hit (PDB entry 3NML in this example). This is fllwed by the remaining entries frm the same family in rder f mdel and data quality. 2 P a g e

3 Useful Tips fr searching 1. The search /query can be saved fr future use using the 'Save search' buttn. 2. Yu can chse t add multiple entries int yur basket, which can be dwnladed later withut having t create any user lgin accunt. 3. It is useful t lk at the results frm different viewpints, e.g.: a. I need t knw all the entries returned by the query 'Entries' tab; b. What unique macrmlecules (i.e. prtein/dna/rna) are fund in these entries? 'Macrmlecules' tab; c. What srt f cmpunds are assciated with the entries? 'Cmpunds' tab; d. What prtein families d these entries belng? 'Prtein families' tab. Search Exercises Last week Nbel prize in Chemistry 2015 was awarded jintly t Tmas Lindahl, Paul Mdrich and Aziz Sancar "fr mechanistic studies f DNA repair". 3 P a g e

4 Their research has been fcused n the three main areas described belw: a. Base excisin repair - Base excisin repairs DNA when a base f a nucletide is damaged, fr example cytsine b. Nucletide excisin repairs DNA-injuries caused by UV radiatin r carcingenic substances like thse fund in cigarette smke. c. Mismatch repair - When DNA is cpied during cell divisin, mismatching nucletides are smetimes incrprated int the new strand. Out f a thusand such mistakes, mismatch repair fixes all but ne. Exercise 1: Using the searchbx at the tp f the PDBe hmepage ( search fr the fllwing terms Base excisin repair (categrised under GO prcess) What are the prteins that are invlved in the base excisin repair prcess? Hw many f the prteins cme frm Human? Hw many structures are there which represent a cmplex between DNA and prtein? Refine yur query further by chsing fr DNA/prtein cmplex frm the left-hand panel f yur results (check under Assembly cmpsitin).click n the prtein families view and find ut hw many structures in the PDB belng t Prtein family: AlkA_N. Which is the best representative structure in this prtein family? Nucletide excisin repair, DNA incisin (categrised under GO prcess) What prtein is respnsible fr the DNA incisin? Is it an enzyme? (check if there are EC numbers) What are the types f interacting mlecules? (e.g. Prtein/DNA/RNA) 4 P a g e

5 Which is the best representative structure fr this prtein in the PDB archive? (click the Macrmlecules tab). muts gene What is the name f the DNA mismatch repair prtein encded by the muts gene? What are the surce rganism f these prtein structures that are present in the PDB? Name the Pfam families and the CATH and SCOP class fr these prteins (check the left hand pane f the search result fr the answer) 5 P a g e

6 Explring a PDB entry Things t remember A typical PDB entry cntains 3D crdinates f the macrmlecular structures that are experimentally derived using X-ray/NMR/electrn micrscpy. It als cntains infrmatin abut secndary structure, bilgical assemblies, sequence mapping infrmatin (UniPrt fr prtein and GenBank fr RNA) fr the prteins and nucleic acids that are present in the entry. The PDB entry can be further explred fr binding envirnment f ligands and ther small mlecules. The infrmatin frm a PDB entry is structured int five majr sectins n the PDBe website t make the data easier t brwse. 6 P a g e

7 Every PDB entry page cmes with a prtfli f images - displaying the cntents f the entry frm varius structural, functinal and chemical perspectives. The citatin page nt nly prvides infrmatin abut primary and assciated publicatins related t the entry, it als displays figures and figure legends fr pen access publicatins. The 'Structure analysis' sectin enables yu t interactively explre prteins in 1D/2D/3D layut. The 'Ligands and Envirnments' sectin lists all the chemically distinct ligands that are present in a particular PDB entry and shws their binding sites. There are several different dwnlad ptins and file frmats present frm a PDB entry page. In addtin t the PDB archive files, every entry page prvides dwnlad ptins fr bilgical assembly files (which can be instantly viewed using any visualisatin tl like Chimera, pyml etc.), sequence files and SIFTS infrmatin. Exercise 2: Quick facts abut influenza: The influenza virus particle is made up f the viral RNA genme wrapped in a lipid membrane. The membrane, r envelpe, cntains three different kinds f viral prteins. The hemagglutinin mlecule (HA) attaches t cell receptrs and initiates the prcess f virus entry int cells. Sialic acid is present n many cell surface prteins as well as n the viral glycprteins; it is the cell receptr t which influenza virus attaches via the HA prtein. The neuraminidase prtein (NA) remves sialic acid frm glycprteins. An imprtant functin f the NA prtein is t remve sialic acid frm glycprteins. Sialic acid is present n many cell surface prteins as well as n the viral glycprteins; it is the cell receptr t which influenza virus attaches via the HA prtein. The sialic acids n the HA and NA are remved as the prteins mve t the cell surface thrugh the secretry pathway. Newly released virus particles can still ptentially aggregate by binding f an HA t sialic acid present n the cell surface. The essential nature f the NA fr virus prductin has been explited t develp new drugs designed t inhibit viral release. 7 P a g e

8 Search and explre the PDB entries 4b7j, 2c4a, 3ti3 and 3b7e cntaining the structure f the neuraminidase enzyme. (pdbe.rg/4b7j, pdbe.rg/2c4a, pdbe.rg/3ti3, pdbe.rg/3b7e) Frm the functin and bilgy sectin f PDB entry 2c4a find ut the bichemical reactin catalysed by neuraminidase. What is the EC number fr the enzyme? What is the CATH dmain classificatin fr all the 4 entries? Explre the Mlecule details sectin fr PDB entry 4b7j. Find the lcatin and identity f the amin residue that cvalently binds t NAG A 521 (N-Acetyl D- Glucsamine) in the 1D/2D/3D alignment f the prtein.(checkut the regins with the clured dts n the 1D representatin f chain A lk ut fr ASN residue lurking arund). Des the residue NAG always bind t the same amin acid type in all the 4 entries? What is the UniPrt cverage fr PDB entry 4b7e? (g t the mlecular details sectin) Find ut ther prtein structures in PDB which share similar 3D fld with the entry 4b7e. (g t mlecular details and then click fr similar 3D structures ). What is the strain f the influenza virus used in PDB entry 3ti3? Which f the entries have pen surce citatin infrmatin? (check pdbe.rg/3ti3, pdbe.rg/4b7j) What is the preferred assembly type fr the neuraminidase enzyme in all the structures? (check the Assembly cmpsitin under structural details) Analyse the binding envirnment fr ligands G39 (Oseltamivir), LNV (Laninamivir), SIA (Sialic acid), ZMR (Zanamivir). Which ne is the natural substrate fr neuraminidase enzyme? Cmpare the chemical structure f Sialic acid with the ther three Ligands. Hw d they differ? D yu think the neuraminidase enzyme will be able t carry ut its sialidase activity in cases where it is bund t Oseltamivir, Laninamivir, Zanamivir? 8 P a g e

9 Validatin Tutrial Mre Help PDBe: Searching the Prtein Data Bank ( PDBe: Explring a Prtein Data Bank (PDB) entry PDBeFld: Search fr a structurally hmlgus prtein ( ( PDBePISA: Identifying and interpreting the likely bilgical assemblies f a prtein PDBeChem: Searching fr small mlecules and small mlecule fragments structure ( ( 9 P a g e

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