2v3j

The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase

Method: X-RAY DIFFRACTION D_max: 65.4 Å Quality: GOOD

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1. Protein Identity and Related Structures Protein Identity & Related Structures

ESSENTIAL FOR MITOTIC GROWTH 1

SACCHAROMYCES CEREVISIAE

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–252	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7.5；25% PEG4K, 0.2M LI2SO4, 0.1M TRIS PH7.5, 20% GLYCEROL	Resolution 2.00 Å R-free 0.271

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 2V3J	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2V3K The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase Deposited 2007-06-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–252（252 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2 SAM S-ADENOSYLMETHIONINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；25% PEG4K, 0.2M LI2SO4, 0.1M TRIS PH7.5, 20% GLYCEROL, pH 7.50	Resolution 2.00 Å R-free 0.247
3OII Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine Deposited 2010-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–252（252 aa） Chain B 1–252（252 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.05M Ammonium Sulfate, 0.05M Bis-Tris, 30% Pentaerythritol ethoxylate, 20% glycerol, pH 6.5, Vapor diffusion, hanging drop, temperature 293K	Resolution 1.85 Å R-free 0.216
3OIJ Crystal structure of Saccharomyces Cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 2 molecules of cognate RNA Deposited 2010-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: tetrameric	Chain A 1–252（252 aa） Chain B 1–252（252 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；0.05M MES, 15mM MgS04, 7% PEG 4000, 20% glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.00 Å R-free 0.260
3OIN Crystal structure of Saccharomyces cerevisiae Nep1/Emg1 bound to S-adenosylhomocysteine and 1 molecule of cognate RNA Deposited 2010-08-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Homooligomer；Protein × 2 PDB declaration: trimeric	Chain A 1–252（252 aa） Chain B 1–252（252 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；0.1M HEPES, 10% PEG 6000, 20% glycerol, pH 7.0, Vapor diffusion, hanging drop, temperature 293K	Resolution 1.90 Å R-free 0.230
5TZS Architecture of the yeast small subunit processome Deposited 2016-11-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 52 PDB declaration: 58-meric	Chain j 1–252（252 aa） Chain k 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE；Incubated 10 seconds on the grid before blotting (blot time 2.0 seconds, blot force 0) and freezing.	Resolution 5.10 Å
5WLC The complete structure of the small subunit processome Deposited 2017-07-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 67 PDB declaration: 70-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
5WYJ Cryo-EM structure of the 90S small subunit pre-ribosome (Dhr1-depleted, Enp1-TAP, state 1) Deposited 2017-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 64-meric	Chain E1 1–252（252 aa） Chain E2 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.70 Å
5WYK Cryo-EM structure of the 90S small subunit pre-ribosome (Mtr4-depleted, Enp1-TAP) Deposited 2017-01-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain E1 1–252（252 aa） Chain E2 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE；blot for 2 seconds before plunging	Resolution 4.50 Å
6KE6 3.4 angstrom cryo-EM structure of yeast 90S small subunit preribosome Deposited 2019-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE；wait 30s and blot 2s before plunging	Resolution 3.40 Å
6LQP Cryo-EM structure of 90S small subunit preribosomes in transition states (State A) Deposited 2020-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
6LQQ Cryo-EM structure of 90S small subunit preribosomes in transition states (State B) Deposited 2020-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 70-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
6LQR Cryo-EM structure of 90S small subunit preribosomes in transition states (State C) Deposited 2020-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 68-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.60 Å
6LQS Cryo-EM structure of 90S small subunit preribosomes in transition states (State D) Deposited 2020-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 76 PDB declaration: 79-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6LQT Cryo-EM structure of 90S small subunit preribosomes in transition states (State E) Deposited 2020-01-14	Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
6LQU Cryo-EM structure of 90S small subunit preribosomes in transition states (State A1) Deposited 2020-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.70 Å
6LQV Cryo-EM structure of 90S small subunit preribosomes in transition states (State C1) Deposited 2020-01-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6ZQA Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state A (Poly-Ala) Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 57 PDB declaration: 60-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
6ZQB Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state B2 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.90 Å
6ZQC Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Pre-A1 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6ZQD Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Post-A1 Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 63 PDB declaration: 66-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
6ZQE Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-A (Poly-Ala) Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 62-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.10 Å
6ZQF Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-B (Poly-Ala) Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 39 PDB declaration: 42-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.90 Å
6ZQG Cryo-EM structure of the 90S pre-ribosome from Saccharomyces cerevisiae, state Dis-C Deposited 2020-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 39	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7AJT Cryo-EM structure of the 90S-exosome super-complex (state Pre-A1-exosome) Deposited 2020-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 83-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7AJU Cryo-EM structure of the 90S-exosome super-complex (state Post-A1-exosome) Deposited 2020-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 74 PDB declaration: 78-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	ZN ZINC ION × 3 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
7D4I Cryo-EM structure of 90S small ribosomal precursors complex with the DEAH-box RNA helicase Dhr1 (State F) Deposited 2020-09-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 79 PDB declaration: 82-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7D5S Cryo-EM structure of 90S preribosome with inactive Utp24 (state A2) Deposited 2020-09-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.60 Å
7D63 Cryo-EM structure of 90S preribosome with inactive Utp24 (state C) Deposited 2020-09-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain RG 1–252（252 aa） Chain RH 1–252（252 aa）	Not recorded	ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 12.30 Å
7SUK Structure of Bfr2-Lcp5 Complex Observed in the Small Subunit Processome Isolated from R2TP-depleted Yeast Cells Deposited 2021-11-17	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 70-meric	Chain SJ 16–251（236 aa） Chain SK 16–251（236 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.99 Å
9G33 Stalled 90S - Utp23-Krr1-deltaC3 Deposited 2024-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 62 PDB declaration: 65-meric	Chain JF 1–252（252 aa） Chain JG 1–252（252 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9N6V SSU processome maturation and disassembly, State A Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 25 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.16 Å
9N6W SSU processome maturation and disassembly, State A* Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 25 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.05 Å
9N6X SSU processome maturation and disassembly, State B Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 34 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.71 Å
9N6Y SSU processome maturation and disassembly, State C Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 34 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.65 Å
9N6Z SSU processome maturation and disassembly, State D Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.74 Å
9N70 SSU processome maturation and disassembly, State E Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 69 PDB declaration: 72-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.17 Å
9N72 SSU processome maturation and disassembly, State F Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 70 PDB declaration: 73-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.94 Å
9N73 SSU processome maturation and disassembly, State G Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 71 PDB declaration: 74-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.96 Å
9N74 SSU processome maturation and disassembly, State H Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 68 PDB declaration: 71-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 39 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.65 Å
9N75 SSU processome maturation and disassembly, State I Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 65 PDB declaration: 68-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 59 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 3 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.01 Å
9N76 SSU processome maturation and disassembly, State J Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 67-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 38 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9N77 SSU processome maturation and disassembly, State K Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 64-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 48 ZN ZINC ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.94 Å
9N78 SSU processome maturation and disassembly, State L Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 59-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.17 Å
9N79 SSU processome maturation and disassembly, State M Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 42 PDB declaration: 45-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.93 Å
9N7A SSU processome maturation and disassembly, State N Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 36 PDB declaration: 39-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.84 Å
9N7B SSU processome maturation and disassembly, State O Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 34 PDB declaration: 37-meric	Chain SJ 1–252（252 aa） Chain SK 1–252（252 aa）	Not recorded	MG MAGNESIUM ION × 47 ZN ZINC ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.25 Å

46 other PDB entries and 46 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	EMG1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–252； UniProt 1–252

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2v3j
Deposition date deposition_date	2007-06-18
Structure title title	The yeast ribosome synthesis factor Emg1 alpha beta knot fold methyltransferase
Keywords keywords	;EMG1, RRNA PROCESSING, NUCLEAR PROTEIN, RIBONUCLEOPROTEIN, RIBOSOME BIOGENESIS, ALPHA/BETA KNOT FOLD METHYLTRANSFERASE, RIBOSOMAL PROTEIN ;; RIBOSOMAL PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	18.62 Å
Radius of gyration Rg (electron density) rg_electron	17.46 Å
Forward intensity I(0) i0	11163400.00
Molecular weight molecular_weight	24775.0 kDa
Excluded volume excluded_volume	31030 Å³
Envelope volume envelope_volume	36630 Å³
Hydration-shell volume shell_volume	17578 Å³
Envelope diameter envelope_diameter	66.5 Å
Shell Rg shell_rg	23.64 Å
Envelope Rg envelope_rg	17.87 Å
Shape Rg shape_rg	17.47 Å
Total Rg total_rg	18.42 Å
Total atoms total_atoms	1716
Residues n_residues	212
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	65.4 Å
Rg (real space) rg_real	18.53 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.1160e+07
I(0) uncertainty (real space) i0_real_error	1.2940e+05
Rg (reciprocal space) rg_reciprocal	18.54 Å
I(0) (reciprocal space) i0_reciprocal	11160000.0000
Solution quality estimate total_estimate	0.7768
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.300
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2500000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.699; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	ESSENTIAL FOR MITOTIC GROWTH 1
Molecular weight formula_weight	29046.7 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1941

MVEDSRVRDALKGGDQKALPASLVPQAPPVLTSKDKITKRMIVVLAMASLETHKISSNGPGGDKYVLLNCDDHQGLLKKMGRDISEARPDITHQCLLTLLDSPINKAGKLQVYIQTSRGILIEVNPTVRIPRTFKRFSGLMVQLLHKLSIRSVNSEEKLLKVIKNPITDHLPTKCRKVTLSFDAPVIRVQDYIEKLDDDESICVFVGAMARGKDNFADEYVDEKVGLSNYPLSASVACSKFCHGAEDAWNILHHHHHH

来源 Source

来源生物 organism	SACCHAROMYCES CEREVISIAE
通用名 common_name	;BAKER'S YEAST ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	225

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2v3ja1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.116 — alpha/beta knot
Superfamily Superfamily superfamily	c.116.1 — alpha/beta knot
Family Family family	c.116.1.6 — EMG1/NEP1-like

CATH v4.4 (1 domains)

Domain ID domain_id	2v3jA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1280 — Alpha/beta knot
Homologous superfamily homologous superfamily	10 — SPOUT methyltransferase, trefoil knot domain

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8. Citations (1)

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Unit-cell length a length_a	42.479 Å
Unit-cell length b length_b	76.614 Å
Unit-cell length c length_c	87.561 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	19.010 Å
R factor r_factor	0.2190
R_work r_work	0.2170
R_free r_free	0.2710

fit	/app/data/saxs_computation/v3/2v3j/2v3j.fit
pddf	/app/data/pr_computation/v3/2v3j/2v3j.pr.out
profile	/app/data/saxs_computation/v3/2v3j/2v3j.dat