SAXSdb — 8yfe

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

;5'-3' exoribonuclease ;

Komagataella phaffii

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–994 Chain C； UniProt 1–994	Mutation：D233A, D235A	Decapping nuclease × 2 （F2QLF5）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；EMGP2	Resolution 3.47 Å

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 8YFE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YF5 Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex Deposited 2024-02-24	Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain A 1–994（994 aa） Chain C 1–994（994 aa）	Mutation：D233A, D235A Mutation：D233A, D235A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；EMGP2	Resolution 3.78 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain R 1–994（994 aa）	Mutation：E203Q, E205Q, D233N, D235N, D330N	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；EMGP2	Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain R 1–994（994 aa）	Mutation：E203Q, E205Q, D233N, D235N, D330N	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；EMGP2	Resolution 3.40 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F2QV79_KOMPC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–994； UniProt 1–994 Author chain C； PDBConstruct 1–994； UniProt 1–994

Decapping nuclease

Komagataella phaffii

UniProt F2QLF5

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain B； UniProt 1–381 Chain D； UniProt 1–381	Mutation：E213A, D215A,D233N	;5'-3' exoribonuclease ; × 2 （F2QV79）	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.5 cryo-EM vitrification conditions：Cryogen ETHANE；EMGP2	Resolution 3.47 Å

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 8YFE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8YF5 Cryo EM structure of Komagataella phaffii Rat1-Rai1-Rtt103 complex Deposited 2024-02-24	Different mutation/modification Different oligomeric state Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain B 1–381（381 aa） Chain D 1–381（381 aa）	Mutation：E213A, D215A Mutation：E213A, D215A	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；EMGP2	Resolution 3.78 Å
8YFQ Cryo EM structure of Komagataella phaffii RNAPII-Rat1-Rai1 pre-termination complex Deposited 2024-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 14 PDB declaration: heptadecameric	Chain S 1–381（381 aa）	Mutation：E213A, D215A	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；EMGP2	Resolution 3.30 Å
8YFR Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex bound within the RNAPII cleft Deposited 2024-02-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 14 PDB declaration: tetradecameric	Chain S 1–381（381 aa）	Mutation：E213A, D215A	ZN ZINC ION × 8 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；EMGP2	Resolution 3.40 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	F2QLF5_KOMPC
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–384； UniProt 1–381 Author chain D； PDBConstruct 4–384； UniProt 1–381

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8yfe
Deposition date deposition_date	2024-02-24
Structure title title	Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex
Keywords keywords	transcription termination, RNA polymerase II, TRANSCRIPTION; TRANSCRIPTION
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	48.99 Å
Radius of gyration Rg (electron density) rg_electron	48.48 Å
Forward intensity I(0) i0	834878000.00
Molecular weight molecular_weight	245180.0 kDa
Excluded volume excluded_volume	308960 Å³
Envelope volume envelope_volume	431040 Å³
Hydration-shell volume shell_volume	74504 Å³
Envelope diameter envelope_diameter	153.5 Å
Shell Rg shell_rg	51.62 Å
Envelope Rg envelope_rg	47.44 Å
Shape Rg shape_rg	48.46 Å
Total Rg total_rg	48.67 Å
Total atoms total_atoms	17315
Residues n_residues	2107
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	155.7 Å
Rg (real space) rg_real	48.86 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	8.3490e+08
I(0) uncertainty (real space) i0_real_error	1.6180e+07
Rg (reciprocal space) rg_reciprocal	48.99 Å
I(0) (reciprocal space) i0_reciprocal	835000000.0000
Solution quality estimate total_estimate	0.8893
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	63.3 Å
Skewness Skewness skewness	0.154
Kurtosis Kurtosis kurtosis	-0.703
Angular range angular_range	— – 0.1600 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	151900000.0000
Real-space data points n_real_points	33
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.696

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	;5'-3' exoribonuclease ;
Molecular weight formula_weight	115314.5 kDa
EC 编号 ec_number	3.1.13.-
Mutation mutation	D233A, D235A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	17315

MGVPALFRWLSRKYPKIISPVIQDEDVDIDGESRPTRYEDPNPNGELDNLYLDMNGIVHPCSHPEHKPVPETEDEMMLDVFAYTENVIMMARPRKVIYIAVDGVAPRAKMNQQRSRRFRSAQDAKDANEKKAAELKEMEKKGEIIDDAIKNKKTWDSNAITPGTPFMHRLADSLRYWAAYKLTTDPGWSGIEVIISDASVPGEGEHKIMSYVRSLRSSPKHDPNTTHCIYGLAAALIFLGLATHEPHFKILREDVFAQDKKSYSLQDQLRMTDIERQELKDKKTPFLWLHLNILREYLQIELNVPGLSFPFDLEKSIDDWVFICFFCGNDFLPHLPSLDVRDNSITTLVTIWKQILPTMKGYLTTDGYLNLPAVERLLAELAKKEDYIFRKRYEDEKRSLENQKRRKLAQEQSSARSQNAPNISTGKDKAPLTPNQNIPLYTTSGESVGIKMTDSEMVNNSALITKANEANKSIAELLKQNLQNEINKKRKISNEEQEVVKESVEEVVEEEDDVLVTSDPEDSSTEILIPKNEEIRLWEPGYRKRYYETKFHTKDPQKVKKIARNMVQKYIEGVSWVLLYYYQGCPSWNWYYPYHYAPFAADFVNLSELKIEFVEGTPFRPYEQLMSVLPAASSHNLPDVFRSLMSDANSEIIDFYPEEFPLDMNGKKVIWQAIPLLPFIDENRLLKAVQSKYDQLTEDEKFRNTNRSEILVLGRSHSHYPTLVKELYEEGKDSYEFQVDSSGVSGVAIKLQSFDRSGVLRLPVKQLEGYRHYPDISNRDFLMVEFKQLPKSHAKSMILSGLIPHLRRLTQEDKDSILYGGTNFYGRNRFSPEENADFKQYIGPHGKSQYLPRQGGYKAFIQIHSDEAKGHRHGIYHGGSHTETEFRRGGGYHQHGNRGGRGGYQGNQGYQANSGGYQNSYQGSYQGGYRGGYQGGSQGRYQAGYQSGYQGGYQGEYKNGYQGGYQGNQGNQGYNRQTYNASKSGTLPMKRRHNSGPSSGLEVLFQ

来源 Source

来源生物 organism	Komagataella phaffii
NCBI Class编号 ncbi_taxonomy_id	460519
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Decapping nuclease
Molecular weight formula_weight	44596.0 kDa
EC 编号 ec_number	3.6.1.-
Mutation mutation	E213A, D215A,D233N
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

GPGMSKEKILPLAARSKKAMLRQPKQVAYFSRDLNYKTHPDRSNLSYYYLPDGDIDNSIDLSVGSKHFLLGDSVELSKLDPILLALKEIEKESGAKTKDRIITWRGIMRKLLTLPYDSEEDFVLDVVSFDGQLFIQFNVPYLKSKDVQKQGDTEFHKKLQFSGYKFEKMATLPKPWPECTRKEIDSRAKSKCNNIEQYGAIVRTGISRIKILIGGAVACTADYYDENDPLSRYIELKTTRTINQYKDMIAFEKKLFRTWAQCFLLGIPKIIYGFRDDNCILRTVEEFSTNDIPLMVKNNPLNEQPKKENCYMSSINFYGAVVEWLNESVKDDQVWKLSYAKRNRQYLVLKEVTDENEKQQIVDSAIPAWFKEWRSELRNSEGNI

来源 Source

来源生物 organism	Komagataella phaffii
NCBI Class编号 ncbi_taxonomy_id	460519
宿主生物 host_organism	Escherichia coli KRX

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.47 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	526250

fit	/app/data/saxs_computation/yf/8yfe/8yfe.fit
pddf	/app/data/pr_computation/yf/8yfe/8yfe.pr.out
profile	/app/data/saxs_computation/yf/8yfe/8yfe.dat

Cryo EM structure of Komagataella phaffii Rat1-Rai1 complex

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

;5'-3' exoribonuclease ;

State in the Current Structure

Other States of the Same Protein in the Database

Decapping nuclease

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)