1IPR seminar, 2016-02-19

Search and view
3DEM structuresin databanks

Hirofumi Suzuki

PDBj / IPR, Osaka univ.

I am ...

2Once upon a time...
• Namba-lab@IIAR, Morikawa-lab@BERI, etc.
• Single particle analyses research

Flagellar motor base
2004, Suzuki et al.

DNA clamp loading
2005, Miyata et al.

Present:• in PDBj• EM Navigator, Yorodumi, Omokage search ...

We are ...

3PDBj• @IPR, Osaka-univ.
• a member of wwPDB

http://pdbj.org

wwPDB• = RCSB-PDB + PDBe+ PDBj + BMRB
• runs PDB• helps EMDB & BMRB

http://wwpdb.org

Questions

Q1: Are you using EM?
(including EM sample, EM data, etc)

4Questions

Q2: Do you know
“EM Navigator”?

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PDB & EMDBPDB & EMDB

methodmaindata

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PDB

EMDB

variousEM

atomic model

3D map（≒ED map）

atom 1
atom 2…
voxels 1,2,3…

num. ofentries~110,000~4,000

New Deposition System

EMDB/BMRB checkbox

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EMDataBank.org

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PDBj contribution for EMDBJapanese serverdata annotated by Japanese staff

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New EM Navigator& Yorodumi

EM Navigator

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moviesearchstatistics

individualdata

Yorodumi

EMDB map + PDB model

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active site & entity
information• EM map + atomic model• Sites (ligand binding, mutation, etc)
• Biological assembly, crystal packing, NMR
ensemble• & many others

New versions
EM Navigator

Yorodumi

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New movie interface
Rotation by mouse
Tiled & synchronizedmultiple movies

Rotation by finger
on a touch device

15

Molecular viewer interface

Simplified EM Map
with PDB model
EMDB-6553 + PDB-3jch

PDB model + ED map(PDB-3cl0)
full-res. EM map interface,under developing16

Projections & sections

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For each the data(except for some hugeraw tomogram)can see backgroundnoise in sections
can peep (盗み見)...
• type of real-spacemask• CTF amplitude
correction• etc.

Statistics

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Microscope
hit-chart

Resolution vs.
temperature

Softwareyearly trends

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Omokage search

Omokage search

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Typical structure search (e.g. Structure Navigator of PDBj)
Anysimilardata?

ABCD
Sequence,
2nd. structure,
etc.

PDB

Comparison& search

User

Atomic model

Omokage searchAnysimilar
data?

EMDB

3DEM map

UserPDBAtomic model(shape only)

SAS dummy
atom model

Comparison& search

SASBDBDot model by vector quantization“dot model” by qvol & qpdb in Situs package（Situs： famous software for “3D fitting” of EM data）

3D-map
EMDB-1003

Atomic model
PDB-1ml5

Each data -> represent with 50 dots-> compare with “dots model” instead of structure

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iDR profile comparison

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model

sort bylengthdistancesof all pairs

50 dots
1225 pairs
Suzuki et al. bioinformatics, 2015

Omokage search

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file upload

ID input box

Sample dataSearch results
RNAP II@25A res.

EMDBentries

PDBentries

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similarity
score“view fitting”
link to gmfit

gmfitFitting by gmfit

25Side view

Dr. T. Kawabata

Test case with GroEL reconstruction

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particle images
from “EMDB test image data”
http://www.ebi.ac.uk/pdbe/emdb/test_data.html
subject of this test

initial modelrefinement #1

refinement #13

Search result

Top >50 data, GroEL only27

Virus capsid

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rice dwarf virus capsid(イネ萎縮ウイルスの殻)

960 chains

Small DNA fragment29

searchfor DNA

proteins
foundfittingby gmfit

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RNAProteinProtein

Function within shapes

protein translation

Green, Curr Biol., 2000

Bensaccount at en.
wikipedia / CC-BY-3.0.

Molecular mimicry (分子擬態)

Find molecular mimicry

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TuTu

Tu

Tu

Tu

G

G

Tu

EF-G structures found by search for EF-Tu complex

Fit protein on RNA

protein fits
RNA

Fitting of PDB 1ob2 + PDB-1elo by gmfit

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Enjoy 3DEM data& shape similarity
Special thanks to• all DB staffs• all DB depositors• all users