SAXSdb — 5m0r

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

integrase

Maedi visna virus (strain KV1772)

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–DNA Homooligomer Protein × 16 DNA 6 PDB declaration: 22-meric（22） Consistent with all polymer counts	Chain A； UniProt 821–1101 Chain B； UniProt 821–1101 Chain C； UniProt 821–1101 Chain D； UniProt 821–1101 Chain E； UniProt 821–1101 Chain F； UniProt 821–1101 Chain G； UniProt 821–1101 Chain H； UniProt 821–1101 Chain I； UniProt 821–1101 Chain J； UniProt 821–1101 Chain K； UniProt 821–1101 Chain L； UniProt 821–1101 Chain M； UniProt 821–1101 Chain N； UniProt 821–1101 Chain O； UniProt 821–1101 Chain P； UniProt 821–1101	Fragment：UNP residues 821-1101	vDNA, non-transfered strand × 2 vDNA-tDNA, transferred strand, joined to a model tDNA × 2 tDNA × 2	ELECTRON MICROSCOPY cryo-EM buffer：pH 6.5 cryo-EM vitrification conditions：Cryogen ETHANE；To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s followed by plunging into liquid ethane.	Resolution 8.20 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 5M0R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain B 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain E 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain F 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.28 Å R-free 0.253
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain C 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain D 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain E 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain F 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.28 Å R-free 0.253
3HPG Visna virus integrase (residues 1-219) in complex with LEDGF IBD: examples of open integrase dimer-dimer interfaces Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain B 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain C 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039 Chain D 823–1039（217 aa） Fragment：N-terminal and catalytic core domains, UNP residues 823-1039	Not recorded	ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.6；291 K；25-30% Jeffamine M600, 100mM Bis-Tris propane-HCl, pH6.6, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 3.28 Å R-free 0.253
3HPH Closed tetramer of Visna virus integrase (residues 1-219) in complex with LEDGF IBD Deposited 2009-06-04	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 823–1039（217 aa） Fragment：N-terminal and catalytic domains, UNP residues 923-1039 Chain B 823–1039（217 aa） Fragment：N-terminal and catalytic domains, UNP residues 923-1039 Chain C 823–1039（217 aa） Fragment：N-terminal and catalytic domains, UNP residues 923-1039 Chain D 823–1039（217 aa） Fragment：N-terminal and catalytic domains, UNP residues 923-1039	Not recorded	ZN ZINC ION × 4 GOL GLYCEROL × 4 PO4 PHOSPHATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.7-0.9M (NH4)2HPO4, 2.5% Jeffamine M600,100mM Bis-Tris propane-HCl, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.64 Å R-free 0.253
5LLJ Maedi-Visna virus (MVV) integrase C-terminal domain (residues 220-276) Deposited 2016-07-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1039–1096（58 aa） Chain B 1039–1096（58 aa）	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M potassium sodium tartrate 0.1M BTP pH 7.5 20% PEG-3350	Resolution 1.78 Å R-free 0.234
5T3A Maedi-Visna virus (MVV) integrase CCD-CTD (residues 60-275) Deposited 2016-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 880–1101（222 aa）	Not recorded	ACT ACETATE ION × 6 MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；0.1M Mes pH6.0, 15-100mM calcium acetate and 15-21% PEG 400	Resolution 2.50 Å R-free 0.240
7U32 MVV cleaved synaptic complex (CSC) intasome at 3.4 A resolution Deposited 2022-02-25	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 16 PDB declaration: eicosameric	Chain A 1226–1506（281 aa） Chain B 1226–1506（281 aa） Chain C 1226–1506（281 aa） Chain D 1226–1506（281 aa） Chain E 1226–1506（281 aa） Chain F 1226–1506（281 aa） Chain G 1226–1506（281 aa） Chain H 1226–1506（281 aa） Chain I 1226–1506（281 aa） Chain J 1226–1506（281 aa） Chain K 1226–1506（281 aa） Chain L 1226–1506（281 aa） Chain M 1226–1506（281 aa） Chain N 1226–1506（281 aa） Chain O 1226–1506（281 aa） Chain P 1226–1506（281 aa）	Not recorded	ZN ZINC ION × 12 CA CALCIUM ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE；Cryo-EM grids were prepared by freezing using a manual plunger in cold room at 4C	Resolution 3.46 Å
7Z1Z MVV strand transfer complex (STC) intasome in complex with LEDGF/p75 at 3.5 A resolution Deposited 2022-02-25	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 18 PDB declaration: 24-meric	Chain A 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain B 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain C 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain D 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain E 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain F 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain G 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain H 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain I 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain J 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain K 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain L 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain M 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain N 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain O 821–1101（281 aa） Fragment：UNP residues 821-1101 Chain P 821–1101（281 aa） Fragment：UNP residues 821-1101	Not recorded	ZN ZINC ION × 12	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；310 mM NaCl, 3 mM CaCl2, 25 mM BisTris-HCl, pH 6.5. cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7ZPP Cryo-EM structure of the MVV CSC intasome at 4.5A resolution Deposited 2022-04-28	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Homooligomer；Protein × 16 PDB declaration: eicosameric	Chain A 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain B 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain C 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain D 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain E 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain F 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain G 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain H 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain I 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain J 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain K 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain L 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain M 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain N 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain O 1226–1506（281 aa） Fragment：UNP residues 821-1101 Chain P 1226–1506（281 aa） Fragment：UNP residues 821-1101	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 6.5；1 M NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl, pH 6.5 cryo-EM vitrification conditions Cryogen ETHANE；To lower salt concentration before plunge-freezing, the grids were blotted for 0.5 s, immediately hydrated with a 4-ul drop of 200 mM NaCl, 3 mM CaCl2 and 25 mM BisTris-HCl pH 6.5 and blotted again for 2.5 s followed by plunging into liquid ethane.	Resolution 4.50 Å

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	POL_VILVK
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–281； UniProt 821–1101 Author chain B； PDBConstruct 1–281； UniProt 821–1101 Author chain C； PDBConstruct 1–281； UniProt 821–1101 Author chain D； PDBConstruct 1–281； UniProt 821–1101 Author chain E； PDBConstruct 1–281； UniProt 821–1101 Author chain F； PDBConstruct 1–281； UniProt 821–1101 Author chain G； PDBConstruct 1–281； UniProt 821–1101 Author chain H； PDBConstruct 1–281； UniProt 821–1101 Author chain I； PDBConstruct 1–281； UniProt 821–1101 Author chain J； PDBConstruct 1–281； UniProt 821–1101 Author chain K； PDBConstruct 1–281； UniProt 821–1101 Author chain L； PDBConstruct 1–281； UniProt 821–1101 Author chain M； PDBConstruct 1–281； UniProt 821–1101 Author chain N； PDBConstruct 1–281； UniProt 821–1101 Author chain O； PDBConstruct 1–281； UniProt 821–1101 Author chain P； PDBConstruct 1–281； UniProt 821–1101

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	5m0r
Deposition date deposition_date	2016-10-05
Structure title title	Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex
Keywords keywords	retrovirus, lentivirus, integrase, DNA-binding, Zn-binding, RNAseH fold, hydrolase; HYDROLASE
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	59.75 Å
Radius of gyration Rg (electron density) rg_electron	60.76 Å
Forward intensity I(0) i0	3880970000.00
Molecular weight molecular_weight	495690.0 kDa
Excluded volume excluded_volume	608060 Å³
Envelope volume envelope_volume	927910 Å³
Hydration-shell volume shell_volume	127210 Å³
Envelope diameter envelope_diameter	200.2 Å
Shell Rg shell_rg	62.51 Å
Envelope Rg envelope_rg	58.66 Å
Shape Rg shape_rg	60.80 Å
Total Rg total_rg	60.67 Å
Total atoms total_atoms	34774
Residues n_residues	4064
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	191.5 Å
Rg (real space) rg_real	59.68 Å
Rg uncertainty (real space) rg_real_error	1.75 Å
I(0) (real space) i0_real	3.8810e+09
I(0) uncertainty (real space) i0_real_error	8.0450e+07
Rg (reciprocal space) rg_reciprocal	59.79 Å
I(0) (reciprocal space) i0_reciprocal	3882000000.0000
Solution quality estimate total_estimate	0.8508
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	73.6 Å
Skewness Skewness skewness	0.289
Kurtosis Kurtosis kurtosis	-0.420
Angular range angular_range	— – 0.1300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	291200000.0000
Real-space data points n_real_points	27
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.926; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.297

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	integrase
Molecular weight formula_weight	32368.8 kDa
EC 编号 ec_number	3.4.23.-,2.7.7.49,3.1.26.13,3.1.13.2,3.6.1.23,2.7.7.-,3.1.-.-
Source method src_method	man
Copy count entity_count	16

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Atom count atom_count	34774

WIENIPLAEEEHNKWHQDAVSLHLEFGIPRTAAEDIVQQCDVCQENKMPSTLRGSNKRGIDHWQVDYTHYEDKIILVWVETNSGLIYAERVKGETGQEFRVQTMKWYAMFAPKSLQSDNGPAFVAESTQLLMKYLGIEHTTGIPWNPQSQALVERTHQTLKNTLEKLIPMFNAFESALAGTLITLNIKRKGGLGTSPMDIFIFNKEQQRIQQQSKSKQEKIRFCYYRTRKRGHPGEWQGPTQVLWGGDGAIVVKDRGTDRYLVIANKDVKFIPPPKEIQKE

来源 Source

来源生物 organism	Maedi visna virus (strain KV1772)
通用名 common_name	MVV
NCBI Class编号 ncbi_taxonomy_id	36374
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	vDNA, non-transfered strand
Molecular weight formula_weight	6456.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	Q,S

GCTGCGAGATCCGCTCCGGTG

Entity 3 Entity 3 polymer

Description description	vDNA-tDNA, transferred strand, joined to a model tDNA
Molecular weight formula_weight	15387.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	R,T

AACACCGGAGCGGATCTCGCAGTCGACCACCCTAATCAAGTTTTTTGGGG

Entity 4 Entity 4 polymer

Description description	tDNA
Molecular weight formula_weight	7073.6 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	U,V

CCCCAAAAAACTTGATTAGGGTG

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8. Citations (1)

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Resolution resolution	8.20 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	37021

fit	/app/data/saxs_computation/m0/5m0r/5m0r.fit
pddf	/app/data/pr_computation/m0/5m0r/5m0r.pr.out
profile	/app/data/saxs_computation/m0/5m0r/5m0r.dat

Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex

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

integrase

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (4)

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

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)