SAXSdb — 9k6h

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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 3 RNA 1 PDB declaration: pentameric（5） Consistent with all polymer counts	Chain A； UniProt 2–1275	Not recorded	Genomic DNA (top strand) × 1 Genomic DNA (bottom strand) × 1 Complementary DNA × 1 Template RNA × 1 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

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 9K6H	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
8SXT Structure of LINE-1 ORF2p with template:primer hybrid Deposited 2023-05-24	Different construct Different oligomeric state 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 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
8SXU Structure of LINE-1 ORF2p with an oligo(A) template Deposited 2023-05-24	Different construct Different oligomeric state Different ligand/ion Different experimental conditions 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 construct Different oligomeric state 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 construct 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 construct 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 construct 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 construct 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 ligand/ion 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 3.30 Å
9K6I Structure of full-length human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid Deposited 2024-10-22	Different ligand/ion 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	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1274； UniProt 2–1275

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	9k6h
Deposition date deposition_date	2024-10-22
最后修订 last_revision	2025-10-22
Structure title title	Structure of human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+
Keywords keywords	Endonuclease, Reverse transcriptase, GENE REGULATION; GENE REGULATION
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	35.12 Å
Radius of gyration Rg (electron density) rg_electron	34.63 Å
Forward intensity I(0) i0	316746000.00
Molecular weight molecular_weight	138200.0 kDa
Excluded volume excluded_volume	170750 Å³
Envelope volume envelope_volume	222000 Å³
Hydration-shell volume shell_volume	52354 Å³
Envelope diameter envelope_diameter	131.8 Å
Shell Rg shell_rg	42.10 Å
Envelope Rg envelope_rg	34.54 Å
Shape Rg shape_rg	34.61 Å
Total Rg total_rg	35.20 Å
Total atoms total_atoms	9651
Residues n_residues	1082
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	119.0 Å
Rg (real space) rg_real	35.01 Å
Rg uncertainty (real space) rg_real_error	1.08 Å
I(0) (real space) i0_real	3.1670e+08
I(0) uncertainty (real space) i0_real_error	5.6380e+06
Rg (reciprocal space) rg_reciprocal	35.08 Å
I(0) (reciprocal space) i0_reciprocal	316800000.0000
Solution quality estimate total_estimate	0.8845
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	42.3 Å
Skewness Skewness skewness	0.227
Kurtosis Kurtosis kurtosis	-0.411
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	48550000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.841; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.971

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	LINE-1 retrotransposable element ORF2 protein
Molecular weight formula_weight	149153.1 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
Atom count atom_count	9651

TGSTSHITILTLNINGLNSAIKRHRLASWIKSQDPSVCCIQETHLTCRDTHRLKIKGWRKIYQANGKQKKAGVAILVSDKTDFKPTKIKRDKEGHYIMVKGSIQQEELTILNIYAPNTGAPRFIKQVLSDLQRDLDSHTLIMGDFNTPLSTLDRSTRQKVNKDTQELNSALHQADLIDIYRTLHPKSTEYTFFSAPHHTYSKIDHIVGSKALLSKCKRTEIITNYLSDHSAIKLELRIKNLTQSRSTTWKLNNLLLNDYWVHNEMKAEIKMFFETNENKDTTYQNLWDAFKAVCRGKFIALNAYKRKQERSKIDTLTSQLKELEKQEQTHSKASRRQEITKIRAELKEIETQKTLQKINESRSWFFERINKIDRPLARLIKKKREKNQIDTIKNDKGDITTDPTEIQTTIREYYKHLYANKLENLEEMDTFLDTYTLPRLNQEEVESLNRPITGSEIVAIINSLPTKKSPGPDGFTAEFYQRYKEELVPFLLKLFQSIEKEGILPNSFYEASIILIPKPGRDTTKKENFRPISLMNIDAKILNKILANRIQQHIKKLIHHDQVGFIPGMQGWFNIRKSINVIQHINRAKDKNHMIISIDAEKAFDKIQQPFMLKTLNKLGIDGTYFKIIRAIYDKPTANIILNGQKLEAFPLKTGTRQGCPLSPLLFNIVLEVLARAIRQEKEIKGIQLGKEEVKLSLFADDMIVYLENPIVSAQNLLKLISNFSKVSGYKINVQKSQAFLYTNNRQTESQIMGELPFTIASKRIKYLGIQLTRDVKDLFKENYKPLLKEIKEETNKWKNIPCSWVGRINIVKMAILPKVIYRFNAIPIKLPMTFFTELEKTTLKFIWNQKRARIAKSILSQKNKAGGITLPDFKLYYKATVTKTAWYWYQNRDIDQWNRTEPSEIMPHIYNYLIFDKPEKNKQWGKDSLFNKWCWENWLAICRKLKLDPFLTPYTKINSRWIKDLNVKPKTIKTLEENLGITIQDIGVGKDFMSKTPKAMATKDKIDKWDLIKLKSFCTAKETTIRVNRQPTTWEKIFATYSSDKGLISRIYNELKQIYKKKTNNPIKKWAKDMNRHFSKEDIYAAKKHMKKCSSSLAIREMQIKTTMRYHLTPVRMAIIKKSGNNRCWRGCGEIGTLLHCWWDCKLVQPLWKSVWRFLRDLELEIPFDPAIPLLGIYPNEYKSCCYKDTCTRMFIAALFTIAKTWNQPKCPTMIDWIKKMWHIYTMEYYAAIKNDEFISFVGTWMKLETIILSKLSQEQKTKHRIFSLIGGN

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	Trichoplusia ni

Entity 2 Entity 2 polymer

Description description	Genomic DNA (top strand)
Molecular weight formula_weight	6027.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	B

AAAAAAAAAAAACCCCCCCC

Entity 3 Entity 3 polymer

Description description	Genomic DNA (bottom strand)
Molecular weight formula_weight	3605.4 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

TTTTTTTTTTTT

Entity 4 Entity 4 polymer

Description description	Complementary DNA
Molecular weight formula_weight	3087.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AAAAAAAAAA

Entity 5 Entity 5 polymer

Description description	Template RNA
Molecular weight formula_weight	3629.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polyribonucleotide
Chain IDs strand_id	E

UUUUUUUUUUUU

Entity 6 Entity 6 non-polymer

Description description	;2'-DEOXYADENOSINE 5'-TRIPHOSPHATE ;
Molecular weight formula_weight	491.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 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	3.00 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	268644

fit	/app/data/saxs_computation/k6/9k6h/9k6h.fit
pddf	/app/data/pr_computation/k6/9k6h/9k6h.pr.out
profile	/app/data/saxs_computation/k6/9k6h/9k6h.dat

Structure of human LINE-1 ORF2p with endogenous DNA and RNA/cDNA hybrid bound to dNTP and Mn2+

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)