SAXSdb — 8sxt

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

LINE-1 retrotransposable element ORF2 protein

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	Other combination Monomer Protein × 1 DNA 1 RNA 1 PDB declaration: trimeric（3） Consistent with all polymer counts	Chain A； UniProt 1–1275	Not recorded	DNA primer × 1 RNA template × 1 TTP THYMIDINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer：pH 7.6；20mM HEPES pH 7.6, 150mM NaCl, 2mM MgOAc, 2mM DTT, 2mM dTTP cryo-EM vitrification conditions：Cryogen ETHANE；Manually blotted from the back	Resolution 3.30 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 8SXT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
7N8K LINE-1 endonuclease domain complex with Mg Deposited 2021-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–238（238 aa）	Not recorded	MG MAGNESIUM ION × 1 ACT ACETATE ION × 3 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；298 K；0.1M LiSO4; 26% PEG 2000 MME	Resolution 2.01 Å R-free 0.236
7N8K LINE-1 endonuclease domain complex with Mg Deposited 2021-06-15	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–238（238 aa）	Not recorded	MG MAGNESIUM ION × 1 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；298 K；0.1M LiSO4; 26% PEG 2000 MME	Resolution 2.01 Å R-free 0.236
7N8S LINE-1 endonuclease domain complex with DNA Deposited 2021-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–238（238 aa）	Mutation：D145A, Y226K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.5；298 K；0.2M NH4 CH3 CO2; 15% PEG 4000	Resolution 2.79 Å R-free 0.322
7N94 LINE-1 endonuclease domain complex with DNA Deposited 2021-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–238（238 aa）	Mutation：D145A, Y226K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；0.1M MES pH 6.0, 0.2M NaCl, 30% Jeffamine ED-2003	Resolution 2.85 Å R-free 0.280
7N94 LINE-1 endonuclease domain complex with DNA Deposited 2021-06-16	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1–238（238 aa）	Mutation：D145A, Y226K	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 6；293 K；0.1M MES pH 6.0, 0.2M NaCl, 30% Jeffamine ED-2003	Resolution 2.85 Å R-free 0.280
8SXU Structure of LINE-1 ORF2p with an oligo(A) template Deposited 2023-05-24	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric	Chain A 1–1275（1275 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；20mM HEPES pH 7.6, 150mM NaCl, 2mM MgOAc, 2mM DTT, 2mM dTTP cryo-EM vitrification conditions Cryogen ETHANE；Manually blotted from the back	Resolution 3.66 Å
8UW3 Human LINE-1 retrotransposon ORF2 protein engaged with template RNA in elongation state Deposited 2023-11-06	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1–1275（1275 aa）	Not recorded	TTP THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9HDO The Human LINE-1 ORF2p target-primed reverse transcription complex Deposited 2024-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric	Chain A 1–1275（1275 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9HDP The Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in a closed conformation Deposited 2024-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric	Chain A 1–1275（1275 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.50 Å
9HDQ The Human LINE-1 ORF2p target-primed reverse transcription complex with the fingers domain in an open conformation Deposited 2024-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric	Chain A 1–1275（1275 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.45 Å
9HDR Human LINE-1 ORF2p target-primed reverse transcription complex with EN domain resolved Deposited 2024-11-12	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: heptameric	Chain A 1–1275（1275 aa）	Not recorded	MG MAGNESIUM ION × 1 ZN ZINC ION × 1 D3T 2',3'-DIDEOXY-THYMIDINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
9K6G Structure of human LINE-1 ORF2p with endogenous dsDNA and RNA/cDNA hybrid Deposited 2024-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–1275（1274 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES pH 7.0, 500 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.30 Å
9K6H Structure of human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+ Deposited 2024-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–1275（1274 aa）	Not recorded	DTP 2'-DEOXYADENOSINE 5'-TRIPHOSPHATE × 1 ZN ZINC ION × 1 MN MANGANESE (II) ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES pH 7.0, 500 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9K6I Structure of full-length human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid Deposited 2024-10-22	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: pentameric	Chain A 2–1275（1274 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES pH 7.0, 500 mM NaCl, 1 mM DTT cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å

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

View Construct and Data Evidence

UniProt name	LORF2_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–1275； UniProt 1–1275

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	8sxt
Deposition date deposition_date	2023-05-24
Structure title title	Structure of LINE-1 ORF2p with template:primer hybrid
Keywords keywords	reverse transcriptase, LINE-1, RNA BINDING PROTEIN, RNA BINDING PROTEIN-RNA-DNA complex; RNA BINDING PROTEIN/RNA/DNA
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	30.37 Å
Radius of gyration Rg (electron density) rg_electron	29.92 Å
Forward intensity I(0) i0	130071000.00
Molecular weight molecular_weight	90879.0 kDa
Excluded volume excluded_volume	114160 Å³
Envelope volume envelope_volume	149080 Å³
Hydration-shell volume shell_volume	40718 Å³
Envelope diameter envelope_diameter	104.4 Å
Shell Rg shell_rg	37.72 Å
Envelope Rg envelope_rg	30.02 Å
Shape Rg shape_rg	29.91 Å
Total Rg total_rg	30.68 Å
Total atoms total_atoms	6382
Residues n_residues	744
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	97.1 Å
Rg (real space) rg_real	30.25 Å
Rg uncertainty (real space) rg_real_error	0.71 Å
I(0) (real space) i0_real	1.3010e+08
I(0) uncertainty (real space) i0_real_error	1.9110e+06
Rg (reciprocal space) rg_reciprocal	30.30 Å
I(0) (reciprocal space) i0_reciprocal	130100000.0000
Solution quality estimate total_estimate	0.6871
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	37.3 Å
Skewness Skewness skewness	0.211
Kurtosis Kurtosis kurtosis	-0.464
Angular range angular_range	— – 0.2600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	33830000.0000
Real-space data points n_real_points	53
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 0.077; Positv: 1.000; Valcen: 1.000; Smooth: 0.954

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	DNA primer
Molecular weight formula_weight	3975.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B
Atom count atom_count	6382

GCGAAAATTTCGC

Entity 2 Entity 2 polymer

Description description	RNA template
Molecular weight formula_weight	5444.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	C

GUGAGCGAAAUUUUCGC

Entity 3 Entity 3 polymer

Description description	LINE-1 retrotransposable element ORF2 protein
Molecular weight formula_weight	149252.3 kDa
EC 编号 ec_number	2.7.7.49,3.1.21.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

MTGSNSHITILTLNVNGLNSPIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSILDRSTRQKVNKDTQELNSALHQTDLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELRIKNLTQSRSTTWKLNNLLLNDYWVHNEMKAEIKMFFETNENKDTTYQNLWDAFKAVCRGKFIALNAYKRKQERSKIDTLTSQLKELEKQEQTHSKASRRQEITKIRAELKEIETQKTLQKINESRSWFFERINKIDRPLARLIKKKREKNQIDTIKNDKGDITTDPTEIQTTIREYYKHLYANKLENLEEMDTFLDTYTLPRLNQEEVESLNRPITGSEIVAIINSLPTKKSPGPDGFTAEFYQRYKEELVPFLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTTKKENFRPISLMNIDAKILNKILANRIQQHIKKLIHHDQVGFIPGMQGWFNIRKSINVIQHINRAKDKNHVIISIDAEKAFDKIQQPFMLKTLNKLGIDGMYLKIIRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNIVLEVLARAIRQEKEIKGIQLGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYNNNRQTESQIMGELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEDTNKWKNIPCSWVGRINIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFIWNQKRARIAKSILSQKNKAGGITLPDFKLYYKATVTKTAWYWYQNRDIDQWNRTEPSEIMPHIYNYLIFDKPEKNKQWGKDSLLNKWCWENWLAICRKLKLDPFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKTPKAMATKDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYKKKTNNPIKKWAKDMNRHFSKEDIYAAKKHMKKCSSSLAIREMQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLVHCWWDCKLVQPLWKSVWRFLRDLELEIPFDPAIPLLGIYPKDYKSCCYKDTCTRMFIAALFTIAKTWNQPNCPTMIDWIKKMWHIYTMEYYAAIKNDEFISFVGTWMKLETIILSKLSQEQKTKHRIFSLIGGN

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 4 Entity 4 non-polymer

Description description	THYMIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	482.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

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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	3.30 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	430198

fit	/app/data/saxs_computation/sx/8sxt/8sxt.fit
pddf	/app/data/pr_computation/sx/8sxt/8sxt.pr.out
profile	/app/data/saxs_computation/sx/8sxt/8sxt.dat

Structure of LINE-1 ORF2p with template:primer hybrid

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

LINE-1 retrotransposable element ORF2 protein

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)