1zmf

C domain of human cyclophilin-33(hcyp33)

Method: X-RAY DIFFRACTION D_max: 48.6 Å Quality: GOOD

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

Peptidyl-prolyl cis-trans isomerase E

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 137–301	Fragment：residues 137-301	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 1.88 Å R-free 0.225

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 1ZMF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2CQB Solution Structure of the RNA recognition motif in Peptidyl-prolyl cis-trans isomerase E Deposited 2005-05-19	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–89（89 aa） Fragment：RNA recognition motif	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.16mM PROTEIN U-15N,13C; 20mM d-Tris-HCL(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O \| 90% H2O/10% D2O	Resolution not provided
2KU7 Solution structure of MLL1 PHD3-Cyp33 RRM chimeric protein Deposited 2010-02-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–82（81 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298.2 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.3-0.5 mM [U-100% 13C; U-100% 15N] MLL PHD3-Cyp33 RRM, 20 mM sodium phosphate, 50 mM sodium chloride, 0.4 mM DSS, 93% H2O/7% D2O \| 93% H2O/7% D2O	Resolution not provided
2KYX Solution structure of the RRM domain of CYP33 Deposited 2010-06-09	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 3–83（81 aa） Fragment：UNP Residues 3-83	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.9；303 K；Pressure ambient NMR sample composition 25 mM potassium phosphate, 50 mM sodium chloride, 1 mM DTT, 1 mM sodium azide, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
2R99 Crystal structure of cyclophilin ABH-like domain of human peptidylprolyl isomerase E isoform 1 Deposited 2007-09-12	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 131–301（171 aa） Fragment：Cyclophilin domain: Residues 131-301	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；298 K；34% PEG 8000, 0.2M Ammonium sulfate, 0.1M Bis-Tris pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K	Resolution 1.61 Å R-free 0.196
3LPY Crystal structure of the RRM domain of CyP33 Deposited 2010-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–82（78 aa） Fragment：N-terminal RRM domain	Not recorded	SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 2.4 M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
3LPY Crystal structure of the RRM domain of CyP33 Deposited 2010-02-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 5–82（78 aa） Fragment：N-terminal RRM domain	Not recorded	SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Hepes-Na, 2.4 M Ammonium Sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.00 Å R-free 0.246
3MDF Crystal structure of the RRM domain of Cyclophilin 33 Deposited 2010-03-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–83（83 aa） Fragment：RNA-RECOGNITION MOTIF (UNP residues:1-83)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；291 K；0.1 M Hepes and 1.0 M tri-sodium dehydrate citrate pH 7.6, Microcapillary, temperature 291K	Resolution 1.85 Å R-free 0.238
3MDF Crystal structure of the RRM domain of Cyclophilin 33 Deposited 2010-03-30	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–83（83 aa） Fragment：RNA-RECOGNITION MOTIF (UNP residues:1-83)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.6；291 K；0.1 M Hepes and 1.0 M tri-sodium dehydrate citrate pH 7.6, Microcapillary, temperature 291K	Resolution 1.85 Å R-free 0.238
3UCH Crystal structure of a peptidyl-prolyl cis-trans isomerase E (PPIE) from Homo sapiens at 2.50 A resolution Deposited 2011-10-26	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 129–301（173 aa） Fragment：residues 129-301	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0% PEG-1000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.214
3UCH Crystal structure of a peptidyl-prolyl cis-trans isomerase E (PPIE) from Homo sapiens at 2.50 A resolution Deposited 2011-10-26	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 129–301（173 aa） Fragment：residues 129-301	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；20.0% PEG-1000, 0.1M TRIS pH 7.0, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.214
5MQF Cryo-EM structure of a human spliceosome activated for step 2 of splicing (C* complex) Deposited 2016-12-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 41 PDB declaration: 41-meric	Chain o 1–301（301 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.90 Å
5YZG The Cryo-EM Structure of Human Catalytic Step I Spliceosome (C complex) at 4.1 angstrom resolution Deposited 2017-12-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain 1 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ADP ADENOSINE-5'-DIPHOSPHATE × 2 ZN ZINC ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.10 Å
5Z56 cryo-EM structure of a human activated spliceosome (mature Bact) at 5.1 angstrom. Deposited 2018-01-17	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: 59-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 13	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH, 150 mM NaCl, 1.5 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.10 Å
5Z57 Cryo-EM structure of the human activated spliceosome (late Bact) at 6.5 angstrom Deposited 2018-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 57-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 ALA ALANINE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 10	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 1.5 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 6.50 Å
6FF7 human Bact spliceosome core structure Deposited 2018-01-03	Different construct 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: 61-meric	Chain o 1–301（301 aa）	Not recorded	ZN ZINC ION × 11 MG MAGNESIUM ION × 5 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.50 Å
6ICZ Cryo-EM structure of a human post-catalytic spliceosome (P complex) at 3.0 angstrom Deposited 2018-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 9 ZN ZINC ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
6ID0 Cryo-EM structure of a human intron lariat spliceosome prior to Prp43 loaded (ILS1 complex) at 2.9 angstrom resolution Deposited 2018-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 38 PDB declaration: 42-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
6ID1 Cryo-EM structure of a human intron lariat spliceosome after Prp43 loaded (ILS2 complex) at 2.9 angstrom resolution Deposited 2018-09-07	Different construct 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: 43-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.86 Å
7A5P Human C Complex Spliceosome - Medium-resolution PERIPHERY Deposited 2020-08-21	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 48-meric	Chain o 1–301（301 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.00 Å
7ABI Human pre-Bact-2 spliceosome Deposited 2020-09-07	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain o 1–301（301 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 8.00 Å
7W59 The cryo-EM structure of human pre-C*-I complex Deposited 2021-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 45 PDB declaration: 50-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 9 ZN ZINC ION × 6 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7W5A The cryo-EM structure of human pre-C*-II complex Deposited 2021-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 54-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 9 ZN ZINC ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
7W5B The cryo-EM structure of human C* complex Deposited 2021-11-29	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 55-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 9 ZN ZINC ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.30 Å
7ZEV Free form of extended Cyp33-RRM Deposited 2022-03-31	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–114（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7ZEW Complex Cyp33-RRM : AAUAAA RNA Deposited 2022-03-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–114（114 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM RNA (5'-R(APAPUPAPAPA)-3'), 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM RNA (5'-R(APAPUPAPAPA)-3'), 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7ZEX Complex Cyp33-RRMdelta alpha : UAAUGUCG RNA Deposited 2022-03-31	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–90（90 aa）	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM RNA (5'-R(UPAPAPUPGPUPCPG)-3'), 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM RNA (5'-R(UPAPAPUPGPUPCPG)-3'), 40 mM sodium chloride, 40 mM sodium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7ZEY Complex Cyp33-RRM : MLL1-PHD3 Deposited 2022-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–114（114 aa） Fragment：RRM (UNP RESIDUES 1-114)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
7ZEZ Trimolecular complex Cyp33-RRMdelta alpha : MLL1-PHD3 : H3K4me3 Deposited 2022-03-31	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain A 1–90（90 aa） Fragment：RRM (UNP RESIDUES 1-90)	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7；310.15 K；Ionic strength (raw mmCIF value) 80；Pressure AMBIENT NMR sample composition 1 mM [U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 50 uM zinc chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O \| 100% D2O NMR sample composition 1 mM PEPTIDYL-PROLYL CIS-TRANS ISOMERASE E, 1 mM [U-100% 13C; U-100% 15N] HISTONE-LYSINE N-METHYLTRANSFERASE 2A, 1 mM HISTONE H3, 40 mM sodium chloride, 40 mM sodium phosphate, 10 uM zinc chloride, 100% D2O \| 100% D2O	Resolution not provided
8C6J Human spliceosomal PM5 C* complex Deposited 2023-01-12	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: 63-meric	Chain CE 1–301（301 aa）	Not recorded	K POTASSIUM ION × 2 MG MAGNESIUM ION × 7 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8CH6 Structure of a late-stage activated spliceosome (BAqr) arrested with a dominant-negative Aquarius mutant (state B complex). Deposited 2023-02-07	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: 59-meric	Chain w 1–301（301 aa）	Not recorded	ZN ZINC ION × 12 IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9；All solutions were sterile-filtered using a 0.22um vacuum filtration unit. cryo-EM vitrification conditions Cryogen ETHANE；Volumes of 4 ul of the concentrated sample were applied to one side of glow-discharged UltrAuFoil 200 2/2 grids (Quantifoil) in a Vitrobot Mark IV (FEI), operated at 4 degrees Celsius and 100% humidity. The grids were blotted for 2s with blotting force 5 and immediately frozen by plunging into liquid ethane.	Resolution 5.90 Å
8I0P The cryo-EM structure of human pre-Bact complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain y 1–301（301 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ZN ZINC ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8I0R The cryo-EM structure of human Bact-I complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 55-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 6 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I0S The cryo-EM structure of human Bact-II complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 46 PDB declaration: 50-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
8I0T The cryo-EM structure of human Bact-III complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 56-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I0U The cryo-EM structure of human Bact-IV complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 53-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
8I0V The cryo-EM structure of human post-Bact complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 51-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 7 ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8I0W The cryo-EM structure of human C complex Deposited 2023-01-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 58-meric	Chain y 1–301（301 aa）	Not recorded	IHP INOSITOL HEXAKISPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 5 ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
9FMD Integrative model of the human post-catalytic spliceosome (P-complex) Deposited 2024-06-05	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: 63-meric	Chain y 1–301（301 aa）	Not recorded	MG MAGNESIUM ION × 6 K POTASSIUM ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ZN ZINC ION × 6 IHP INOSITOL HEXAKISPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å

35 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPIE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–165； UniProt 137–301

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	1zmf
Deposition date deposition_date	2005-05-10
Structure title title	C domain of human cyclophilin-33(hcyp33)
Keywords keywords	Human cyclophilin-33, PPIase, ISOMERASE; ISOMERASE
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	15.43 Å
Radius of gyration Rg (electron density) rg_electron	14.26 Å
Forward intensity I(0) i0	6299150.00
Molecular weight molecular_weight	17803.0 kDa
Excluded volume excluded_volume	22096 Å³
Envelope volume envelope_volume	24015 Å³
Hydration-shell volume shell_volume	13919 Å³
Envelope diameter envelope_diameter	48.3 Å
Shell Rg shell_rg	20.51 Å
Envelope Rg envelope_rg	14.56 Å
Shape Rg shape_rg	14.25 Å
Total Rg total_rg	15.43 Å
Total atoms total_atoms	1249
Residues n_residues	162
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	48.6 Å
Rg (real space) rg_real	15.30 Å
Rg uncertainty (real space) rg_real_error	0.25 Å
I(0) (real space) i0_real	6.2990e+06
I(0) uncertainty (real space) i0_real_error	7.7220e+04
Rg (reciprocal space) rg_reciprocal	15.32 Å
I(0) (reciprocal space) i0_reciprocal	6299000.0000
Solution quality estimate total_estimate	0.8838
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	20.9 Å
Skewness Skewness skewness	0.044
Kurtosis Kurtosis kurtosis	-0.404
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1840000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.840; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.980

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1zmfa_
Class class	b — All beta proteins
Fold Fold fold	b.62 — Cyclophilin-like
Superfamily Superfamily superfamily	b.62.1 — Cyclophilin-like
Family Family family	b.62.1.1 — Cyclophilin (peptidylprolyl isomerase)

CATH v4.4 (1 domains)

Domain ID domain_id	1zmfA00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	100 — Cyclophilin
Homologous superfamily homologous superfamily	10 — Cyclophilin-like

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8. Citations (1)

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Unit-cell length a length_a	66.610 Å
Unit-cell length b length_b	66.610 Å
Unit-cell length c length_c	76.780 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	8

Space group space_group	P 42 21 2
Space-group number int_tables_number	94
Crystal system crystal_system	—

Resolution resolution	1.880 Å
Low-resolution limit resolution_low	47.100 Å
R factor r_factor	0.1720
R_work r_work	0.1690
R_free r_free	0.2250

Description description	Peptidyl-prolyl cis-trans isomerase E
Molecular weight formula_weight	18230.7 kDa
EC 编号 ec_number	5.2.1.8
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1391

C domain of human cyclophilin-33(hcyp33)

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

Peptidyl-prolyl cis-trans isomerase E

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	142

fit	/app/data/saxs_computation/zm/1zmf/1zmf.fit
pddf	/app/data/pr_computation/zm/1zmf/1zmf.pr.out
profile	/app/data/saxs_computation/zm/1zmf/1zmf.dat