Structure-based assembly of protein complexes in yeast

Patrick Aloy, Hugo Ceulemans & Rob Russell*


EMBL Structural & Computational Biology Programme
Meyerhofstrasse 1, 69117 Heidelberg, Germany.
*Tel: +49 6221 387 473; Email: russell@embl.de
Related to:
Structure-based assembly of protein complexes in yeast
Patrick Aloy(1) , Bettina Böttcher(1) , Hugo Ceulemans(1) , Christina Leutwein (2),
Christian Mellwig(1) , Susanne Fischer(1) , Anne-Claude Gavin (2), Peer Bork(1),
Giulio Superti-Furga (2), Luis Serrano(1) and Robert B. Russell(1)*
Science, In Press, 2004.
1. EMBL, 2. Cellzome AG

Cellzome annotated complexes
IDComponentsDescriptionStatus
Chaperonin complexes
073 ERP2 ERP1 EMP24 ERV25p24 complexTemplates for 4 components and 0 interactions. EM quality 3
121 PFD2 PFD3 PFD1 PFD6 PFD5 PFD4prefoldin complexTemplates for 6 components and 10 interactions. EM quality 3
257 CCT4 CCT6 CCT1 CCT2 CCT8 CCT3 CCT7 CCT5 VID27 PLP2CCT complex Templates for 10 components and 29 interactions. EM quality 1
Chromosome dynamics
086 ISW1 RSC6 RSC3 RSC8 RSC1 RSC30 STH1 RSC4 RSC58 SFH1 RSC2 RSC9 ARP9 NPL6 ARP7RSC complexTemplates for 10 components and 10 interactions. EM quality 3
125 SCC1 SMC1 SCC3 SMC3cohesin complexTemplates for 2 components and 1 interactions. EM quality 3
190 MCM19 MCM21 OKP1 MCM22 CTF3 MCM18 MCM16outer kinetochore complex (not the 6-component MCM complex)Templates for 0 components and 0 interactions. EM quality 3
233 SPC97 TUB4 SPC98Spc97/98/Tub4 complex (SPB)Templates for 1 components and 0 interactions. EM quality 3
249 CAC3 CAC2 CAC1chromatin assembly factor-I (CAF-I) complexTemplates for 2 components and 1 interactions. EM quality 3
254 SPC25 NDC80 SPC24 NUF2Ndc80 complexTemplates for 0 components and 0 interactions. EM quality 3
328 BRN1 YCS5 SMC2 SMC4 YCS4condensin complexTemplates for 3 components and 1 interactions. EM quality 3
Cytoskeleton/vesicle structure and dynamics
037 VPS29 VPS26 VPS35 VPS5 VPS17retromer complexTemplates for 3 components and 1 interactions. EM quality 3
071 CHC1 CLC1clathrinTemplates for 1 components and 0 interactions. EM quality 3
079 CDC10 SHS1 CDC12 CDC11 CDC3septin ringTemplates for 4 components and 0 interactions. EM quality 3
081 CAP2 P40563 CAP1F-actin capping protein Templates for 2 components and 1 interactions. EM quality 3
098 VPS54 VPS52 VPS53 VPS51Vps51/52/53/54 complexTemplates for 1 components and 0 interactions. EM quality 3
102 TRS20 TRS85 TRS23 TRS31 BET3 BET5 TRS33TRAPP I complexTemplates for 2 components and 0 interactions. EM quality 3
104 HSE1 VPS27Vps27/Hse1 complexTemplates for 2 components and 1 interactions. EM quality 3
109 VPS8 VPS39 VPS41 VPS18 VPS33 VPS11 VPS16class C Vps complexTemplates for 5 components and 1 interactions. EM quality 3
124 APM3 APL6 APS3 APL5adaptor protein 3 (AP-3) complexTemplates for 4 components and 6 interactions. EM quality 3
147 TOS1 PGK1 RET1 ARF1 SEC26 GLO3 RET2 SEC27 SEC28 SEC21 RET3COP I/coatomer complexTemplates for 9 components and 11 interactions. EM quality 3
153 ARC40 ARP2 ARC15 ARP3 ARC19 ARC18 ARC35Arp2/3 complexTemplates for 7 components and 17 interactions. EM quality 3
175 EXO84 SEC5 SEC3 SEC15 SEC6 EXO70 SEC10 SEC8exocyst complex Templates for 1 components and 0 interactions. EM quality 3
203 APM2 APL2 APS1 APM1 APL4adaptor protein 1 (AP-1) complexTemplates for 5 components and 10 interactions. EM quality 3
236 COG3 COG7 COG1 COG2 COG8 COG6 COG5 COG4COG complex Templates for 1 components and 0 interactions. EM quality 3
250 APL3 APL1 APS2 APM4adaptor protein 2 (AP-2) complexTemplates for 4 components and 6 interactions. EM quality 3
258 VPS15 VPS34 VPS38 VPS30Vps34 complex IITemplates for 2 components and 1 interactions. EM quality 3
DNA replication and repair
072 DPB3 DPB4 POL2 DPB2DNA polymerase II (epsilon)Templates for 3 components and 1 interactions. EM quality 3
150 ORC2 ORC6 ORC3 ORC1 ORC5 ORC4origin recognition complexTemplates for 3 components and 3 interactions. EM quality 3
219 POL12 PRI1 PRI2 POL1 POP2DNA polymerase-primaseTemplates for 3 components and 0 interactions. EM quality 3
Enzymes
002 BAT1 BAT2branched-chain amino acid aminotransferaseTemplates for 2 components and 1 interactions. EM quality 3
010 SER3 PHO12 SER33D-3-phosphoglycerate dehydrogenaseTemplates for 3 components and 1 interactions. EM quality 3
021 BET4 BET2Rab geranylgeranyltransferase IITemplates for 2 components and 1 interactions. EM quality 3
031 TPS1 TPS2 TSL1 TPS3trehalose-6-P-synthaseTemplates for 4 components and 1 interactions. EM quality 3
033 TRP2 TRP3anthranilate synthaseTemplates for 2 components and 1 interactions. EM quality 3
068 KGD2 LPD1 KGD12-oxo-glutarate dehydrogenase holoenzymeTemplates for 3 components and 1 interactions. EM quality 3
092 LCB2 LCB1serine palmitoyltransferaseTemplates for 2 components and 1 interactions. EM quality 3
100 PDB1 CYM1 PDA1 LPD1 PDX1 LAT1pyruvate dehydrogenase complexTemplates for 6 components and 4 interactions. EM quality 3
114 OST4 WBP1 STT3 OST5 OST1 OST6 SWP1 OST3 OST2oligo-saccharyl transferase complexTemplates for 1 components and 0 interactions. EM quality 3
133 QCR1 BRE1 RBS1 QCR2core subcomplex of respiratory chain complex IIITemplates for 4 components and 1 interactions. EM quality 3
199 LYS2 LYS5aminoadipate-semialdehyde dehydrogenaseTemplates for 2 components and 1 interactions. EM quality 3
216 PFK1 PFK26-phosphofructokinase complexTemplates for 2 components and 1 interactions. EM quality 3
237 PHO88 MNN10 MNN8 OLE1 PMR1 PHB2 MNN11 HOC1 MNN9mannosyl transferase complexTemplates for 2 components and 0 interactions. EM quality 3
Nuclear Pore
119 GLE2 NIC96 NUP159 NSP1 NUP82 NUP116Nup116 subcomplex of the nuclear pore complexTemplates for 2 components and 0 interactions. EM quality 3
235 NUP84 NUP145 SEH1 NUP85 NUP120 SEC13Nup84 complex (5 nucleoporins + a COPII coat complex subunit)Templates for 3 components and 1 interactions. EM quality 3
267 NIC96 NUP49 NUP57 NSP1Nps1 subcomplex of the nuclear pore complexTemplates for 2 components and 1 interactions. EM quality 3
Proteolysis, Proteasome, Ub-ligases, degradation
005 CSN5 CSN9 CSN11 CSI1 CSN10COP9/signalosome complexTemplates for 1 components and 0 interactions. EM quality 3
034 ULA1 UBA3Rub1 ubiquitin activator complex (E1)Templates for 2 components and 1 interactions. EM quality 3
069 CDC27 APC11 APC4 CDC26 APC10 CDC23 CDC16 APC9 APC2 APC1 APC5cyclosome/APC (anaphase promoting complex)Templates for 6 components and 4 interactions. EM quality 3
106 PRE7 PRE1 PUP3 PRE4 SCL1 PRE9 PUP2 PRE3 PRE8 PSE1 PRE5 PRE6 PUP1 PRE10 PRE220S proteasome subcomplexTemplates for 15 components and 91 interactions. EM quality 1
148 RPT2 RPN4 RPN6 RPN5 RPT3 RPN9 RPN3 RPN11 UBP6 RPN12 RPT6 HUL5 ECM29 RPN1 RPN10 RPN2 RPT1 RPN13 RPT5 RPT4 RPN8 RPN719S regulatory proteasome subcomplex + assoc. regulatory complexTemplates for 15 components and 36 interactions. EM quality 3
241 YTA10 HMG2 YTA12mAAA proteaseTemplates for 3 components and 1 interactions. EM quality 3
RNA synthesis, transport, processing, degradation
091 CEG1 CET1mRNA capping enzymeTemplates for 2 components and 0 interactions. EM quality 3
094 SEC66 SSS1 SBH1 SEC67 SEC61 SEC63 SEC62translocon complexTemplates for 2 components and 0 interactions. EM quality 3
113 PAF1 HPR1 SPT16 RTF1 CDC73 SPT5 POB3 CTR9 LEO1RNA polymerase II-associated Paf1 complexTemplates for 3 components and 1 interactions. EM quality 3
139 ROX3 MED8 SRB6 SRB8 MED2 SRB7 SRB9 SRB4 HRS1 SOH1 NUT1 SRB5 SRB2 MED6 RGR1 MED11 SRB11 SIN4 MED9 GAL11 MED7 MED4 SRB10 MED1 MED10RNA polymerase II mediator complexTemplates for 6 components and 1 interactions. EM quality 3
145 RPB5 RPB1 RPB7 RPB9 TFG2 RPC10 RPB3 RPB4 SPT5 RPB11 RPB2 RPB10 RPB8 RPB6RNA polymerase IITemplates for 14 components and 36 interactions. EM quality 1
154A RPB5 RPC53 MAF1 RPC11 RPC10 RPC17 RPC25 RPC37 RPC19 RPC31 RPC34 RPC160 RPC128 RPB10 RPB8 RPC40 RPB6 RPC82RNA polymerase IIITemplates for 11 components and 24 interactions. EM quality
154B RPB5 RPA14 RPC10 RPA34 RPA12 RPC19 RPA49 RPB10 RPB8 RPA43 RPA190 RPA135 RPC40 RPB6RNA polymerase I Templates for 10 components and 24 interactions. EM quality
158 PRP9 PRP11 SMB1 SMX2 SMD1 IST3 MSL1 PRP21 SMD3 SMD2 RSE1 HRT2 CUS1 HSH155 CUS2 SME1 HSH49 LEA1 SMX3U2 snRNPTemplates for 15 components and 35 interactions. EM quality 2
160 LUC1 LUC7 PRP42 LUC4 SMB1 SMX2 LUC5 SMD1 LUC3 SNP1 PRP40 SMD3 SMD2 YHC1 PRP39 SME1 SMX3U1 snRNP complexTemplates for 13 components and 25 interactions. EM quality 3
162 PTA1 REF2 PCF11 CFT1 PAB1 RNA15 FIP1 MPE1 PAP1 CFT2 YSH1 RNA14 SSU72 PFS2 Q08553 CLP1 YTH1RNA 3' end processing factorTemplates for 11 components and 2 interactions. EM quality 3
164 CTK2 CTK1 CTK3CTD kinase (check this please)Templates for 2 components and 1 interactions. EM quality 3
167 P39998 DCP2 DCP1mRNA decapping protein complexTemplates for 2 components and 0 interactions. EM quality 3
213 PAN2 PAN3PAB1-dependent poly(A)-nucleaseTemplates for 2 components and 0 interactions. EM quality 3
220 POP5 POP8 POP7 POP4 POP6 RPP1 POP1 POP3truncus communis ribonucleases P/MRPTemplates for 0 components and 0 interactions. EM quality 2
251 SKI8 SKI2 SKI3Ski complexTemplates for 3 components and 2 interactions. EM quality 3
265 CCR4 NOT1 NOT2 NOT4 CAF130 NOT3 CAF40 POP2 NOT5Ccr4/Pop2/Not complex (mRNA deadenylase)Templates for 3 components and 1 interactions. EM quality 3
500 RRP46 RRP43 MTR3 RRP41 RRP42 RRP45 RRP4 RRP40 CSL4 RRP44 RRP6ExosomeTemplates for 0 components and 15 interactions. EM quality 1
Signal transduction
030 BCY1 TPK1 TPK2inactive PKA holoenzymeTemplates for 3 components and 1 interactions. EM quality 3
057 YKU80 YKU70Ku complexTemplates for 2 components and 1 interactions. EM quality 3
Transcriptional regulation/Epigenetic control
001 TFC3 TFC1 TFC6 TFC4 TFC7 TFC8transcription initiation factor IIIc (transcription factor tau)Templates for 3 components and 0 interactions. EM quality 3
029 TOA2 TOA1transcription factor TFIIATemplates for 2 components and 1 interactions. EM quality 3
074 EPL1 ACT1 YNG2 TRA1 ARP4 YAP1 CRZ1 ESA1 EAF3NuA4 histone acetyltransferase complexTemplates for 8 components and 1 interactions. EM quality 3
075 SNF1 SNF4 SIP2Snf-kinase holoenzymeTemplates for 3 components and 0 interactions. EM quality 3
105 SNF5 SNF11 SNF6 SWI3 YAP1 ARP9 CRZ1 SNF12 SWI2 SWI1 TAF30 ARP7SWI/SNF complexTemplates for 9 components and 1 interactions. EM quality 3
108 CPS50 CPS30 CPS25 SET1 CPS35 CPS60 CPS40COMPASS complexTemplates for 5 components and 3 interactions. EM quality 3
131 CDC27 KIN28 TFB1 TFB3 RAD3 SSL2 SSL1 FPR1 TFB2 CCL1 TFB4transcription factor TFIIHTemplates for 8 components and 7 interactions. EM quality 3
136 SPT7 TAF90 SGF29 TAF61 TAF25 SWI7 SPT3 SWI8 SGF73 TAF60 SWI9 TRA1 SPT8 TAF17 SPT20 HFI1SAGA complex Templates for 12 components and 9 interactions. EM quality 3
137 RXT3 SDS3 RCO1 ECM16 SAP30 PHO23 SDS6 SDS16 UME1 RXT1 EAF3HDAC (histone deacetylase C) complexTemplates for 7 components and 1 interactions. EM quality 3
159 FUN19 TAF90 TAF150 TAF61 TAF25 TFIID TAF60 TAF130 TAF40 TAF19 TAF65 TAF48 TAF67 TAF17 TAF47 TAF30transcription factor II-D (TFII-D)Templates for 11 components and 17 interactions. EM quality 3
170 ELP2 ELP5 ELP1 ELP6 ELP3 ELP4Elongator complex Templates for 3 components and 3 interactions. EM quality 3
193 ITC1 ADH1 ISW2Itc1/Isw2 complexTemplates for 2 components and 0 interactions. EM quality 3
200 MAK31 MAK10 MAK3amino acid N-acetyltransferase complexTemplates for 2 components and 0 interactions. EM quality 3
202A MBP1 SWI6MBF complexTemplates for 2 components and 1 interactions. EM quality
202B SWI4 SWI6SBF complexTemplates for 2 components and 1 interactions. EM quality
tRNA Synthetases, protein synthesis, protein secretion
022 SRP101 SRP102signal recognition particle receptor complexTemplates for 2 components and 1 interactions. EM quality 3
023 SRP14 SRP21 SEC65 SRP72 SRP68 SRP54signal recognition particleTemplates for 4 components and 0 interactions. EM quality 3
123 VAR1 MRP21 MRPS9 MRPS5 MRP10 P28817 RSM10 RSM24 MRPS28 MRP1 RSM18 YMR31 RSM23 MRP13 MRPS35 RSM27 MRP4 MRPS2 RSM25 RSM26 RSM7 MRP17 RSM22 MRPS8 MRPS17 P53937 NAM9 MRPS18 P53732 RSM19 PET123 MRPS16 MRP51 MRP2mitochondrial small (40S) ribosomal subunitTemplates for 21 components and 12 interactions. EM quality 3
127 P38286 GCD6 GCD11 GCD2 SUI2 GCN3 GCD7 IST1 RAS1 GCD1 SUI3interacting eIF2 (Sui2/3/4) and eIF2B (Gcd1/2/6/7/Gcn3) complexesTemplates for 7 components and 3 interactions. EM quality 3
138 TIF32 TIF35 HCR1 TIF34 NIP1 SUI1 PRT1 TIF5 SUA7eIF1/eIF3/eIF5 complexTemplates for 7 components and 3 interactions. EM quality 3
177 FRS2 FRS1cytoplasmic phenylalanyl tRNA synthetaseTemplates for 2 components and 1 interactions. EM quality 3
243 ARC1 MES1methionyl tRNA synthetaseTemplates for 2 components and 0 interactions. EM quality 3
Unknown
056 NUC1 P36159?Templates for 2 components and 0 interactions. EM quality 3
065 P53738 Q12463?Templates for 1 components and 0 interactions. EM quality 2
117 P89886 P47089?Templates for 2 components and 0 interactions. EM quality 3
135 P38193 PPH3 PSY2?Templates for 2 components and 0 interactions. EM quality 3
146 ENP1 TSR1 P53251 RIO2 NOB1?Templates for 3 components and 0 interactions. EM quality 1
185 PLO2 HDA1 PLO1?Templates for 3 components and 1 interactions. EM quality 3
191 IPP1 Q07622 ROM2 TUS1?Templates for 4 components and 4 interactions. EM quality 3
198 LTE1 KEL1?Templates for 2 components and 0 interactions. EM quality 3
225 PTC4 Q04007?Templates for 1 components and 0 interactions. EM quality 3


Patrick Aloy