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4fp9

Human MTERF4-NSUN4 protein complex

Method: X-RAY DIFFRACTION Dmax: 208.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

methyltransferase NSUN4

Homo sapiens

UniProt Q96CB9

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain A； UniProt 26–384 Chain C； UniProt 26–384 Chain D； UniProt 26–384 Chain F； UniProt 26–384 Not recorded mTERF domain-containing protein 2 × 4 （Q7Z6M4） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 26–384 Not recorded mTERF domain-containing protein 2 × 1 （Q7Z6M4） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain C； UniProt 26–384 Not recorded mTERF domain-containing protein 2 × 1 （Q7Z6M4） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain D； UniProt 26–384 Not recorded mTERF domain-containing protein 2 × 1 （Q7Z6M4） 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
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain F； UniProt 26–384 Not recorded mTERF domain-containing protein 2 × 1 （Q7Z6M4） 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

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 4FP9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4FZV Crystal structure of the human MTERF4:NSUN4:SAM ternary complex Deposited 2012-07-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 26–384（359 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) 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
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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 14 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 2–360； UniProt 26–384 Author chain C； PDBConstruct 2–360； UniProt 26–384 Author chain D； PDBConstruct 2–360； UniProt 26–384 Author chain F； PDBConstruct 2–360； 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 × 8 PDB declaration: octameric（8） Consistent with protein copy count Chain B； UniProt 47–381 Chain E； UniProt 47–381 Chain G； UniProt 47–381 Chain H； UniProt 47–381 Not recorded methyltransferase NSUN4 × 4 （Q96CB9） 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
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 47–381 Not recorded methyltransferase NSUN4 × 1 （Q96CB9） 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
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain E； UniProt 47–381 Not recorded methyltransferase NSUN4 × 1 （Q96CB9） 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
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain G； UniProt 47–381 Not recorded methyltransferase NSUN4 × 1 （Q96CB9） 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
5 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain H； UniProt 47–381 Not recorded methyltransferase NSUN4 × 1 （Q96CB9） 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

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 4FP9 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4FZV Crystal structure of the human MTERF4:NSUN4:SAM ternary complex Deposited 2012-07-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 92–330（239 aa）
Not recorded 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
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 14 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 1–335； UniProt 47–381 Author chain E； PDBConstruct 1–335； UniProt 47–381 Author chain G； PDBConstruct 1–335； UniProt 47–381 Author chain H； PDBConstruct 1–335； UniProt 47–381

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

SAXS profile for 4fp9

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fp9
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fp9
Deposition date deposition_date2012-06-21
Structure title titleHuman MTERF4-NSUN4 protein complex
Keywords keywordsModification enzyme, TRANSFERASE; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier54.84 Å
Radius of gyration Rg (electron density) rg_electron56.10 Å
Forward intensity I(0) i01008930000.00
Molecular weight molecular_weight266690.0 kDa
Excluded volume excluded_volume335460 ų
Envelope volume envelope_volume502110 ų
Hydration-shell volume shell_volume80588 ų
Envelope diameter envelope_diameter228.4 Å
Shell Rg shell_rg51.75 Å
Envelope Rg envelope_rg57.06 Å
Shape Rg shape_rg55.99 Å
Total Rg total_rg56.33 Å
Total atoms total_atoms18717
Residues n_residues2327
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax208.9 Å
Rg (real space) rg_real55.41 Å
Rg uncertainty (real space) rg_real_error3.35 Å
I(0) (real space) i0_real1.0090e+09
I(0) uncertainty (real space) i0_real_error2.3930e+07
Rg (reciprocal space) rg_reciprocal54.39 Å
I(0) (reciprocal space) i0_reciprocal1007000000.0000
Solution quality estimate total_estimate0.7876
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary64.8 Å
Skewness Skewness skewness0.750
Kurtosis Kurtosis kurtosis0.568
Angular range angular_range— – 0.1450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha44780000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.533; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.942; Smooth: 0.692
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4fp9A01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology240 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4fp9A02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id4fp9C01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology240 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4fp9C02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id4fp9D01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology240 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4fp9D02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
Domain ID domain_id4fp9F01
Class class6 — Special
Architecture architecture20 — Other non-globular
Topology topology240 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily40 —
Domain ID domain_id4fp9F02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily150 — Vaccinia Virus protein VP39
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8. Citations (1)

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9. Files and Curves (10)