8PFR

Mouse RPL39L integrated into the yeast 60S ribosomal subunit

• PDB DOI: https://doi.org/10.2210/pdb8PFR/pdb
• EM Map EMD-17653: EMDB EMDataResource
• NAKB: 8PFR

• Classification: RIBOSOME
• Organism(s): Saccharomyces cerevisiae, Mus musculus
• Expression System: Saccharomyces cerevisiae
• Mutation(s): No 


• Deposited: 2023-06-16 Released: 2024-06-26 
• Deposition Author(s): Rabl, J., Banerjee, A., Boehringer, D., Zavolan, M.
• Funding Organization(s): Swiss National Science Foundation

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 2.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Mouse RPL39L integrated into the yeast 60S ribosomal subunit

Rabl, J., Banerjee, A., Boehringer, D., Zavolan, M.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 40-mer - A1B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1n1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 40-mer - A2B1C1D1E1F1G1H1I1J1K1L1M1N1O1P1Q1R1S1T1U1V1W1X1Y1Z1a1b1c1d1e1f1g1h1i1j1k1l1m1 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content

• Total Structure Weight: 1,933.03 kDa 
• Atom Count: 120,018 
• Modelled Residue Count: 9,385 
• Deposited Residue Count: 10,233 
• Unique protein chains: 40
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L32	B [auth RE]	130	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38061  Go to UniProtKB:  P38061

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L8-A	C [auth LL]	256	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P17076  Go to UniProtKB:  P17076

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L22-A	D [auth QU]	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05749  Go to UniProtKB:  P05749

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L26-A	E [auth QY]	127	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05743  Go to UniProtKB:  P05743

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L2-A	F [auth LF]	254	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX45  Go to UniProtKB:  P0CX45

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L39-like	G [auth RN]	51	Mus musculus	Mutation(s): 0  Gene Names: Rpl39l
UniProt
Find proteins for Q9CQD0 (Mus musculus) Explore Q9CQD0  Go to UniProtKB:  Q9CQD0

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L23-A	H [auth QV]	137	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX41  Go to UniProtKB:  P0CX41

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L13-A	I [auth JT]	199	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q12690  Go to UniProtKB:  Q12690

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L33-A	J [auth RF]	107	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05744  Go to UniProtKB:  P05744

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L9-A	K [auth LM]	191	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05738  Go to UniProtKB:  P05738

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L24-A	L [auth QW]	155	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04449  Go to UniProtKB:  P04449

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L27-A	M [auth QZ]	136	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H6  Go to UniProtKB:  P0C2H6

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L3	N [auth LG]	387	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14126  Go to UniProtKB:  P14126

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-60S ribosomal protein L40	O [auth RO]	128	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CH08  Go to UniProtKB:  P0CH08

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L25	P [auth QX]	142	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P04456  Go to UniProtKB:  P04456

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L14-A	Q [auth JU]	138	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P36105  Go to UniProtKB:  P36105

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L34-A	R [auth RG]	121	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P87262  Go to UniProtKB:  P87262

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L10	S [auth LN]	221	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P41805  Go to UniProtKB:  P41805

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L4-A	T [auth LH]	362	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P10664  Go to UniProtKB:  P10664

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L28	U [auth RA]	149	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02406  Go to UniProtKB:  P02406

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L35-A	V [auth RH]	120	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX84  Go to UniProtKB:  P0CX84

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L42-A	W [auth RQ]	106	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX27  Go to UniProtKB:  P0CX27

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L5	X [auth LI]	297	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26321  Go to UniProtKB:  P26321

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L15-A	Y [auth JV]	204	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05748  Go to UniProtKB:  P05748

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L36-A	Z [auth RI]	100	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05745  Go to UniProtKB:  P05745

Entity ID: 27
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L11-A	AA [auth LO]	174	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0C0W9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C0W9  Go to UniProtKB:  P0C0W9

Entity ID: 28
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L6-A	BA [auth LJ]	176	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02326  Go to UniProtKB:  Q02326

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L29	CA [auth RB]	59	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05747  Go to UniProtKB:  P05747

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L37-A	DA [auth RJ]	88	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49166  Go to UniProtKB:  P49166

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L43-A	EA [auth RT]	92	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX25  Go to UniProtKB:  P0CX25

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L7-A	FA [auth LK]	244	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05737  Go to UniProtKB:  P05737

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L16-A	GA [auth JW]	199	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P26784  Go to UniProtKB:  P26784

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L38	HA [auth RM]	78	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P49167  Go to UniProtKB:  P49167

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L17-A	IA [auth QO]	184	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P05740  Go to UniProtKB:  P05740

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L30	JA [auth RC]	105	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P14120  Go to UniProtKB:  P14120

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L18-A	KA [auth QP]	186	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX49  Go to UniProtKB:  P0CX49

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L19-A	MA [auth QQ]	189	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX82  Go to UniProtKB:  P0CX82

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L31-A	NA [auth RD]	113	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0C2H8  Go to UniProtKB:  P0C2H8

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L20-A	OA [auth QS]	172	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CX23  Go to UniProtKB:  P0CX23

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
60S ribosomal protein L21-A	QA [auth QT]	160	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore Q02753  Go to UniProtKB:  Q02753

Entity ID: 1
Molecule	Chains	Length	Organism	Image
25S rRNA	A	3,396	Saccharomyces cerevisiae

Entity ID: 38
Molecule	Chains	Length	Organism	Image
5.8S rRNA	LA [auth LD]	158	Saccharomyces cerevisiae

Entity ID: 42
Molecule	Chains	Length	Organism	Image
5S rRNA	PA [auth LE]	121	Saccharomyces cerevisiae

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	ID [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
SPD	FF [auth A]	SPERMIDINE C7 H19 N3 ATHGHQPFGPMSJY-UHFFFAOYSA-N
ZN	CI [auth RQ], EI [auth RJ], FI [auth RT], YH [auth RO], ZH [auth RG]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CL	BI [auth RQ], EB [auth A], GG [auth A], HI [auth QO], IC [auth A], MB [auth A], MF [auth A], ND [auth A], NE [auth A], OE [auth A], QB [auth A], QC [auth A], QF [auth A], RC [auth A], SF [auth A], TC [auth A], TG [auth A], UB [auth A], UG [auth A], VD [auth A], VG [auth A], XF [auth A], XH [auth LG], ZC [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	AB [auth A], AC [auth A], AD [auth A], AE [auth A], AF [auth A], AG [auth A], AH [auth A], AI [auth RA], BB [auth A], BC [auth A], BD [auth A], BE [auth A], BF [auth A], BG [auth A], BH [auth A], CB [auth A], CC [auth A], CD [auth A], CE [auth A], CF [auth A], CG [auth A], CH [auth A], DB [auth A], DC [auth A], DD [auth A], DE [auth A], DF [auth A], DG [auth A], DH [auth A], DI [auth RI], EC [auth A], ED [auth A], EE [auth A], EF [auth A], EG [auth A], EH [auth A], FB [auth A], FC [auth A], FD [auth A], FE [auth A], FG [auth A], FH [auth A], GB [auth A], GC [auth A], GD [auth A], GE [auth A], GF [auth A], GH [auth A], GI [auth QO], HB [auth A], HC [auth A], HD [auth A], HE [auth A], HF [auth A], HG [auth A], HH [auth A], IB [auth A], IE [auth A], IF [auth A], IG [auth A], IH [auth A], II [auth LD], JB [auth A], JC [auth A], JD [auth A], JE [auth A], JF [auth A], JG [auth A], JH [auth A], JI [auth LE], KB [auth A], KC [auth A], KD [auth A], KE [auth A], KF [auth A], KG [auth A], KH [auth A], LB [auth A], LC [auth A], LD [auth A], LE [auth A], LF [auth A], LG [auth A], LH [auth A], MC [auth A], MD [auth A], ME [auth A], MG [auth A], MH [auth A], NB [auth A], NC [auth A], NF [auth A], NG [auth A], NH [auth A], OB [auth A], OC [auth A], OD [auth A], OF [auth A], OG [auth A], OH [auth A], PB [auth A], PC [auth A], PD [auth A], PE [auth A], PF [auth A], PG [auth A], PH [auth A], QD [auth A], QE [auth A], QG [auth A], QH [auth A], RA [auth A], RB [auth A], RD [auth A], RE [auth A], RF [auth A], RG [auth A], RH [auth A], SA [auth A], SB [auth A], SC [auth A], SD [auth A], SE [auth A], SG [auth A], SH [auth A], TA [auth A], TB [auth A], TD [auth A], TE [auth A], TF [auth A], TH [auth A], UA [auth A], UC [auth A], UD [auth A], UE [auth A], UF [auth A], UH [auth A], VA [auth A], VB [auth A], VC [auth A], VE [auth A], VF [auth A], VH [auth A], WA [auth A], WB [auth A], WC [auth A], WD [auth A], WE [auth A], WF [auth A], WG [auth A], WH [auth RE], XA [auth A], XB [auth A], XC [auth A], XD [auth A], XE [auth A], XG [auth A], YA [auth A], YB [auth A], YC [auth A], YD [auth A], YE [auth A], YF [auth A], YG [auth A], ZA [auth A], ZB [auth A], ZD [auth A], ZE [auth A], ZF [auth A], ZG [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.15 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-06-26 
Deposition Author(s): Rabl, J., Banerjee, A., Boehringer, D., Zavolan, M.

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Funding Organization	Location	Grant Number
Swiss National Science Foundation	Switzerland	51NF40_141735

Revision History  

• Version 1.0: 2024-06-26
  Type: Initial release