SAXSdb — 4fzv

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

Putative methyltransferase NSUN4

Homo sapiens

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 26–384	Non-standard monomer：Yes (specific site not provided by mmCIF)	mTERF domain-containing protein 2 × 1 （Q7Z6M4） SAM S-ADENOSYLMETHIONINE × 1 FMT FORMIC ACID × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.15 M magnesium formate, 50 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.190

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 4FZV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 26–384（359 aa） Chain C 26–384（359 aa） Chain D 26–384（359 aa） Chain F 26–384（359 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 4 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 26–384（359 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 26–384（359 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 26–384（359 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 26–384（359 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
7O9K Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu Deposited 2021-04-16	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: 69-meric	Chain A1 1–384（384 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 93 SAM S-ADENOSYLMETHIONINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7O9M Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module Deposited 2021-04-16	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: 66-meric	Chain A1 1–384（384 aa）	Not recorded	MG MAGNESIUM ION × 104 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
7ODR State A of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	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: 57-meric	Chain x 1–384（384 aa）	Not recorded	PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 97 K POTASSIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 2.90 Å
7ODS State B of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	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: 58-meric	Chain x 1–384（384 aa）	Not recorded	PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 88 K POTASSIUM ION × 8 N ANY 5'-MONOPHOSPHATE NUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 3.10 Å
7ODT State C of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	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: 58-meric	Chain x 1–384（384 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 95 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 K POTASSIUM ION × 10 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 3.10 Å
7OF0 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset1). Deposited 2021-05-04	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 × 54 PDB declaration: 56-meric	Chain C 1–384（384 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 61	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
7OF3 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset2). Deposited 2021-05-04	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 × 54 PDB declaration: 56-meric	Chain C 1–384（384 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 58 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7OF5 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset2). Deposited 2021-05-04	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: 57-meric	Chain C 1–384（384 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 70 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7OF7 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1). Deposited 2021-05-04	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: 57-meric	Chain C 1–384（384 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 74	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7OIC Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4 Deposited 2021-05-11	Different construct 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 x 1–384（384 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 76 ZN ZINC ION × 3 PNS 4'-PHOSPHOPANTETHEINE × 1 SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7PD3 Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP Deposited 2021-08-04	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 × 58 PDB declaration: 60-meric	Chain x 1–384（384 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 91 PNS 4'-PHOSPHOPANTETHEINE × 1 SAM S-ADENOSYLMETHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8PK0 human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 Deposited 2023-06-23	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: 58-meric	Chain x 1–384（384 aa）	Not recorded	ZN ZINC ION × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 96 K POTASSIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
8QSJ Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 Deposited 2023-10-10	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: 58-meric	Chain x 1–384（384 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 38 FES FE2/S2 (INORGANIC) CLUSTER × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

14 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	NSUN4_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–359； UniProt 26–384

mTERF domain-containing protein 2

Homo sapiens

UniProt Q7Z6M4

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 92–330	Not recorded	Putative methyltransferase NSUN4 × 1 （Q96CB9） SAM S-ADENOSYLMETHIONINE × 1 FMT FORMIC ACID × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 5.5；298 K；0.15 M magnesium formate, 50 mM Bis-Tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.00 Å R-free 0.190

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 4FZV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain B 47–381（335 aa） Chain E 47–381（335 aa） Chain G 47–381（335 aa） Chain H 47–381（335 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 4 SO4 SULFATE ION × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 47–381（335 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 47–381（335 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 47–381（335 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
4FP9 Human MTERF4-NSUN4 protein complex Deposited 2012-06-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 47–381（335 aa）	Not recorded	SAM S-ADENOSYLMETHIONINE × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；294 K；100 mM Bis-Tris [pH 5.5], 400 mM ammonium sulfate, 20-22 % (w/v) polyethylene glycol 3350, and 2 mM dithiothreitol, VAPOR DIFFUSION, temperature 294K	Resolution 2.90 Å R-free 0.246
7O9K Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu Deposited 2021-04-16	Different construct 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: 69-meric	Chain A2 1–381（381 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 93 SAM S-ADENOSYLMETHIONINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7O9M Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module Deposited 2021-04-16	Different construct 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: 66-meric	Chain A2 1–381（381 aa）	Not recorded	MG MAGNESIUM ION × 104 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.60 Å
7ODR State A of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	Different construct 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: 57-meric	Chain y 1–381（381 aa）	Not recorded	PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 97 K POTASSIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 2.90 Å
7ODS State B of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	Different construct 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: 58-meric	Chain y 1–381（381 aa）	Not recorded	PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 88 K POTASSIUM ION × 8 N ANY 5'-MONOPHOSPHATE NUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 3.10 Å
7ODT State C of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30	Different construct 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: 58-meric	Chain y 1–381（381 aa）	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 95 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 K POTASSIUM ION × 10 FES FE2/S2 (INORGANIC) CLUSTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging	Resolution 3.10 Å
7OF0 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset1). Deposited 2021-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain G 1–381（381 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 61	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.20 Å
7OF3 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset2). Deposited 2021-05-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric	Chain G 1–381（381 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 58 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.70 Å
7OF5 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset2). Deposited 2021-05-04	Different construct 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: 57-meric	Chain G 1–381（381 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 70 GTP GUANOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7OF7 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1). Deposited 2021-05-04	Different construct 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: 57-meric	Chain G 1–381（381 aa）	Not recorded	ZN ZINC ION × 3 MG MAGNESIUM ION × 74	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
7OIC Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4 Deposited 2021-05-11	Different construct 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 y 1–381（381 aa）	Not recorded	MG MAGNESIUM ION × 76 ZN ZINC ION × 3 PNS 4'-PHOSPHOPANTETHEINE × 1 SAM S-ADENOSYLMETHIONINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
7PD3 Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP Deposited 2021-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric	Chain y 1–381（381 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 91 PNS 4'-PHOSPHOPANTETHEINE × 1 SAM S-ADENOSYLMETHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8PK0 human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 Deposited 2023-06-23	Different construct 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: 58-meric	Chain y 1–381（381 aa）	Not recorded	ZN ZINC ION × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 96 K POTASSIUM ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.03 Å
8QSJ Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 Deposited 2023-10-10	Different construct 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: 58-meric	Chain y 1–381（381 aa）	Not recorded	ZN ZINC ION × 2 MG MAGNESIUM ION × 38 FES FE2/S2 (INORGANIC) CLUSTER × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å

14 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MTER2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–239； UniProt 92–330

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4fzv
Deposition date deposition_date	2012-07-08
Structure title title	Crystal structure of the human MTERF4:NSUN4:SAM ternary complex
Keywords keywords	MTERF fold, methyltransferase fold, rRNA methyltransferase, mitochondria, TRANSFERASE; TRANSFERASE
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	31.50 Å
Radius of gyration Rg (electron density) rg_electron	31.26 Å
Forward intensity I(0) i0	62907600.00
Molecular weight molecular_weight	60994.0 kDa
Excluded volume excluded_volume	75546 Å³
Envelope volume envelope_volume	98981 Å³
Hydration-shell volume shell_volume	28580 Å³
Envelope diameter envelope_diameter	118.3 Å
Shell Rg shell_rg	34.79 Å
Envelope Rg envelope_rg	32.80 Å
Shape Rg shape_rg	31.36 Å
Total Rg total_rg	31.24 Å
Total atoms total_atoms	4272
Residues n_residues	567
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	113.0 Å
Rg (real space) rg_real	32.08 Å
Rg uncertainty (real space) rg_real_error	1.28 Å
I(0) (real space) i0_real	6.2910e+07
I(0) uncertainty (real space) i0_real_error	1.0390e+06
Rg (reciprocal space) rg_reciprocal	31.84 Å
I(0) (reciprocal space) i0_reciprocal	62890000.0000
Solution quality estimate total_estimate	0.7544
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	110.8 Å
Skewness Skewness skewness	0.710
Kurtosis Kurtosis kurtosis	-0.140
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	12300000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.468; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.563; Smooth: 0.836

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Putative methyltransferase NSUN4
Molecular weight formula_weight	40607.3 kDa
EC 编号 ec_number	2.1.1.-
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	4635

RYKKKWAATEPKFPAVRLALQNFDMTYSVQFGDLWPSIRVSLLSEQKYGALVNNFAAWDHVSAKLEQLSAKDFVNEAISHWELQSEGGQSAAPSPASWACSPNLRCFTFDRGDISRFPPARPGSLGVMEYYLMDAASLLPVLALGLQPGDIVLDLCAAPGGKTLALLQTGCCRNLAANDLSPSRIARLQKILHSYVPEEIRDGNQVRVTSWDGRKWGELEGDTYDRVLVDVPCTTDRHSLHEEENNIFKRSRKKERQILPVLQVQLLAAGLLATKPGGHVVYSTCSLSHLQNEYVVQGAIELLANQYSIQVQVEDLTHFRRVFMDTFCFFSSCQVGELVIPNLMANFGPMYFCKMRRLT

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	mTERF domain-containing protein 2
Molecular weight formula_weight	27045.9 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXQQLLDIISEFILLGLNPEPVCVVLKKSPQLLKLPIMQMRKRSSYLQKLGLGEGKLKRVLYCCPEIFTMRQQDINDTVRLLKEKCLFTVQQVTKILHSCPSVLREDLGQLEYKFQYAYFRMGIKHPDIVKSEYLQYSLTKIKQRHIYLERLGRYQTPDKKGQTQIPNPLLKDILRVSEAEFLARTACTSVEEFQVFKKLLAREEEESESS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	S-ADENOSYLMETHIONINE
Molecular weight formula_weight	398.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	301

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	4fzvA01
Class class	6 — Special
Architecture architecture	20 — Other non-globular
Topology topology	240 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily	40 —

Domain ID domain_id	4fzvA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	150 — Vaccinia Virus protein VP39

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8. Citations (1)

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Unit-cell length a length_a	298.667 Å
Unit-cell length b length_b	53.226 Å
Unit-cell length c length_c	52.963 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	46.815 Å
R factor r_factor	0.1660
R_work r_work	0.1647
R_free r_free	0.1903

fit	/app/data/saxs_computation/fz/4fzv/4fzv.fit
pddf	/app/data/pr_computation/fz/4fzv/4fzv.pr.out
profile	/app/data/saxs_computation/fz/4fzv/4fzv.dat

Crystal structure of the human MTERF4:NSUN4:SAM ternary complex

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

Putative methyltransferase NSUN4

State in the Current Structure

Other States of the Same Protein in the Database

mTERF domain-containing protein 2

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)