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6ccj

NMR structure of the Rous sarcoma virus matrix protein (M domain)

Method: SOLUTION NMR Dmax: 39.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

virus matrix protein

Rous sarcoma virus (strain Prague C)

UniProt P03354

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 2–87 Mutation：M1S No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；305 K；Ionic strength (raw mmCIF value) 0.1；Pressure 1 NMR sample composition：0.5 mM [U-95% 13C; U-95% 15N] RSV MA, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition：.5 mM [U-95% 15N] Matrix protein, 50 mM sodium phosphate, 50 mM sodium chloride, 2 M TCEP, 95% H2O/5% D2O | 95% H2O/5% D2O NMR sample composition：0.5 mM [U-95% 13C] Matrix protein, 50 mM sodium phosphate, 50 mM sodium chloride, 2 mM TCEP, 100% D2O | 100% D2O Resolution not provided

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 6CCJ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1A5V ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND MN CATION Deposited 1998-02-18 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Not recorded MN MANGANESE (II) ION × 2 Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA HEPES, PH 7.5
Resolution 1.90 Å R-free 0.210
1A5V ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 AND MN CATION Deposited 1998-02-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Not recorded MN MANGANESE (II) ION × 2 Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA HEPES, PH 7.5
Resolution 1.90 Å R-free 0.210
1A5W ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 Deposited 1998-02-18 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Not recorded Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6
Resolution 2.00 Å R-free 0.222
1A5X ASV INTEGRASE CORE DOMAIN WITH HIV-1 INTEGRASE INHIBITOR Y3 Deposited 1998-02-18 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Not recorded Y3 4-ACETYLAMINO-5-HYDROXYNAPHTHALENE-2,7-DISULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；20% PEG 4000, 10% ISOPROPANOL, 0.1M HEPES, PH 7.5
Resolution 1.90 Å R-free 0.212
1ASU AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 2% PEG 400, 2M AMMONIUM SULFATE, HEPES PH 7.5 Deposited 1995-08-25 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 624–779（156 aa）
Mutation：INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209) EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.70 Å R-free 0.188
1ASV Avian sarcoma virus integrase catalytic core domain Deposited 1995-08-25 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 624–779（156 aa）
Mutation：INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；pH 5.6
Resolution 2.20 Å R-free 0.234
1ASW AVIAN SARCOMA VIRUS INTEGRASE CATALYTIC CORE DOMAIN CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, HEPES PH 7.5 USING SELENOMETHIONINE SUBSTITUTED PROTEIN; DATA COLLECTED AT-165 DEGREES C Deposited 1995-08-25 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 624–779（156 aa）
Mutation：INS(PRO 48, LEU 49, ARG 50, GLU 51, ASN 208, LEU 209) Non-standard monomer：Yes (specific site not provided by mmCIF) EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 IPA ISOPROPYL ALCOHOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5
Resolution 1.80 Å R-free 0.208
1C0M CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE Deposited 1999-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 621–858（238 aa） Fragment：RESIDUES 49-286
Chain B 621–858（238 aa） Fragment：RESIDUES 49-286
Mutation：F199K Mutation：F199K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION METHOD；pH 7；277 K；PLATE-SHAPED CRYSTALS WERE INFREQUENTLY GROWN BY HANGING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.05M SODIUM CACODYLATE, PH 7.0, 10% PEG 3350, and 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML), HANGING DROP VAPOR DIFFUSION METHOD, temperature 277K
Resolution 2.53 Å R-free 0.279
1C0M CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE Deposited 1999-07-16 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 621–858（238 aa） Fragment：RESIDUES 49-286
Chain D 621–858（238 aa） Fragment：RESIDUES 49-286
Mutation：F199K Mutation：F199K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions HANGING DROP VAPOR DIFFUSION METHOD；pH 7；277 K；PLATE-SHAPED CRYSTALS WERE INFREQUENTLY GROWN BY HANGING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.05M SODIUM CACODYLATE, PH 7.0, 10% PEG 3350, and 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML), HANGING DROP VAPOR DIFFUSION METHOD, temperature 277K
Resolution 2.53 Å R-free 0.279
1C1A CRYSTAL STRUCTURE OF RSV TWO-DOMAIN INTEGRASE Deposited 1999-07-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 621–858（238 aa） Fragment：RESIDUES 49-286
Chain B 621–858（238 aa） Fragment：RESIDUES 49-286
Mutation：F199K Mutation：F199K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions ROD-SHAPED CRYSTALS WERE GROWN BY SITTING DROP VAPOR DIFFUSION METHOD. RESERVOIR SOLUTION CONTAINED 0.050M KCL, 0.01M MGCL2, 0.1M SODIUM CACODYLATE, 0.02M IMIDAZOLE, PH 7.2, 10% PEG3350, AND 20% (V/V) ETHYLENE GLYCOL. THE DROP CONTAINED 1:1 MIXTURE OF RESERVOIR SOLUTION AND PROTEIN (10-15 MG/ML)
Resolution 3.10 Å R-free 0.337
1CXQ ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM AMMONIUM SULFATE Deposited 1999-08-30 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Mutation：INS(P48, L49, R50, E51, N208, L209) EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；2% Peg 400, 2M Ammonium Sulfate, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 1.02 Å R-free 0.157
1CXU 1.42A RESOLUTION ASV INTEGRASE CORE DOMAIN FROM CITRATE Deposited 1999-08-30 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Mutation：INS(P48, L49, R50, E51, N208, L209) CIT CITRIC ACID × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；20% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE, PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.42 Å R-free 0.221
1CZ9 ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN (D64N) FROM CITRATE Deposited 1999-09-01 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Mutation：D64N, INS(P48, L49, R50, E51, N208, L209) SO4 SULFATE ION × 2 CIT CITRIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；20% PEG 4000, 10% ISOPROPANOL, 100 MM CITRATE PH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
Resolution 1.20 Å R-free 0.150
1CZB ATOMIC RESOLUTION ASV INTEGRASE CORE DOMAIN FROM HEPES Deposited 1999-09-01 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 624–779（156 aa） Fragment：CATALYTIC CORE DOMAIN
Mutation：INS(P48, L49, R50, E51, N208, L209) EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；20% PEG 4000, 10% ISOPROPANOL, 100 mM HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Resolution 1.06 Å R-free 0.164
1VSD ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM Deposited 1995-11-29 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 616–771（156 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Non-standard monomer：Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLI-MOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 500 MILLI-MOLAR MGCL2.
Resolution 1.70 Å R-free 0.191
1VSE ASV INTEGRASE CORE DOMAIN WITH MG(II) COFACTOR AND HEPES LIGAND, LOW MG CONCENTRATION FORM Deposited 1995-11-29 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 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Not recorded EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLIMOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 20 MILLIMOLAR MGCL2.
Resolution 2.20 Å R-free 0.201
1VSF ASV INTEGRASE CORE DOMAIN WITH MN(II) COFACTOR AND HEPES LIGAND, HIGH MG CONCENTRATION FORM Deposited 1995-11-29 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 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Not recorded MN MANGANESE (II) ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；pH 7.5 THE PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MILLIMOLAR HEPES PH 7.5. CRYSTALS WERE THEN SOAKED IN 10 MILLIMOLAR MNCL2.
Resolution 2.05 Å R-free 0.189
1VSH ASV INTEGRASE CORE DOMAIN WITH ZN(II) COFACTORS Deposited 1997-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM ZNCL2.
Resolution 1.95 Å
1VSI ASV INTEGRASE CORE DOMAIN WITH CA(II) COFACTOR Deposited 1997-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Non-standard monomer：Yes (specific site not provided by mmCIF) CA CALCIUM ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, 10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM CACL2.
Resolution 2.20 Å
1VSJ ASV INTEGRASE CORE DOMAIN WITH CD(II) COFACTORS Deposited 1997-03-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN, RESIDUES 1 - 4, 52 - 209
Non-standard monomer：Yes (specific site not provided by mmCIF) CD CADMIUM ION × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 20% PEG 4000, N10% ISOPROPANOL, 100 MM HEPES, PH 7.5, THEN SOAKED IN 100 MM CDCL2.
Resolution 2.10 Å
1VSK ASV INTEGRASE CORE DOMAIN D64N MUTATION IN CITRATE BUFFER PH 6.0 Deposited 1998-09-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN
Mutation：D64N No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6
Resolution 2.20 Å R-free 0.249
1VSL ASV INTEGRASE CORE DOMAIN D64N MUTATION WITH ZINC CATION Deposited 1998-09-18 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 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN
Mutation：D64N ZN ZINC ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.6
Resolution 2.20 Å R-free 0.244
1VSM ASV INTEGRASE CORE DOMAIN IN CITRATE BUFFER PH 5.0 Deposited 1998-09-18 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 626–771（146 aa） Fragment：CATALYTIC CORE DOMAIN
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.6；20% PEG 4000, 10% ISOPROPANOL, 0.1M NA CITRATE PH 5.0, pH 5.6
Resolution 2.15 Å R-free 0.238
3TIR Pseudo-atomic model of the Rous Sarcoma Virus capsid hexamer Deposited 2011-08-21 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric
Chain A 240–465（226 aa） Fragment：UNP resides 240-465
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 10.3；291.15 K；2-7 %(w/v) PEG 8000 0.2M CAPS/KOH, pH 10.3, VAPOR DIFFUSION, SITTING DROP, temperature 291.15K
Resolution 4.10 Å R-free 0.391
4FW1 Crystal structure of two-domain RSV INTEGRASE covalently linked with DNA Deposited 2012-06-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1329–1550（222 aa） Fragment：UNP residues 1329-1580
Chain B 1329–1550（222 aa） Fragment：UNP residues 1329-1580
Mutation：S124D, C125A, E157C, R166K, F199K Mutation：S124D, C125A, E157C, R166K, F199K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；5% Ethanol, 10% PEG4,000, 100mM Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.86 Å R-free 0.222
4FW2 Crystal structure of RSV three-domain integrase with disordered N-terminal domain Deposited 2012-06-29 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 1281–1550（270 aa） Fragment：UNP residues 1281-1550
Chain B 1281–1550（270 aa） Fragment：UNP residues 1281-1550
Mutation：C23S, R166K, F199K Mutation：C23S, R166K, F199K No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；20% ethanol, 100 mM imidazole-HCl, and 5% PEG4000, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.65 Å R-free 0.244
5EJK Crystal structure of the Rous sarcoma virus intasome Deposited 2015-11-02 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 Homooligomer；Protein × 8 PDB declaration: hexadecameric
Chain A 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain B 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain C 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain D 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain E 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain F 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain G 1281–1550（270 aa） Fragment：UNP residues 573-842
Chain H 1281–1550（270 aa） Fragment：UNP residues 573-842
Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：C23S, L112M, L135M, L162M, L163M, L188 M, L189M Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 8 W TUNGSTEN ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；293 K；Sodium formate
Resolution 3.80 Å R-free 0.294
5KZ9 Crystal structure of the Rous sarcoma virus matrix protein. Deposited 2016-07-24 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–155（155 aa） Fragment：UNP residues 1-155
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.3；293 K；2.60 M Ammonium formate, 0.20 M Beta-Alanine/KOH pH 10.3
Resolution 2.85 Å R-free 0.239
5KZ9 Crystal structure of the Rous sarcoma virus matrix protein. Deposited 2016-07-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 1–155（155 aa） Fragment：UNP residues 1-155
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.3；293 K；2.60 M Ammonium formate, 0.20 M Beta-Alanine/KOH pH 10.3
Resolution 2.85 Å R-free 0.239
5KZA Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I41 Deposited 2016-07-24 Different construct Different mutation/modification 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 2–102（101 aa） Fragment：UNP residues 2-102
Not recorded NO3 NITRATE ION × 2 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；18%(w/v) PEG 8000, 0.2 M Succinic acid/KOH pH 5.5, 1.0 M Ammonium nitrate
Resolution 1.86 Å R-free 0.210
5KZA Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I41 Deposited 2016-07-24 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 2–102（101 aa） Fragment：UNP residues 2-102
Not recorded NO3 NITRATE ION × 4 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；291.15 K；18%(w/v) PEG 8000, 0.2 M Succinic acid/KOH pH 5.5, 1.0 M Ammonium nitrate
Resolution 1.86 Å R-free 0.210
5KZB Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I4122 Deposited 2016-07-24 Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 2–102（101 aa） Fragment：UNP residues 2-102
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；291.15 K；0.6 M Malonic acid /KOH pH 9.1, 0.1 M Boric acid /KOH pH 9.1
Resolution 3.20 Å R-free 0.249
5KZB Crystal structure of the Rous sarcoma virus matrix protein (aa 2-102). Space group I4122 Deposited 2016-07-24 Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 2–102（101 aa） Fragment：UNP residues 2-102
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.1；291.15 K；0.6 M Malonic acid /KOH pH 9.1, 0.1 M Boric acid /KOH pH 9.1
Resolution 3.20 Å R-free 0.249
6CE5 NMR structure of the Rous sarcoma virus matrix protein (M-domain) in the presence of myo-inositol hexakisphosphate Deposited 2018-02-11 Different construct Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–87（87 aa）
Mutation：M1S No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 0.05；Pressure 1
NMR sample composition 0.5 mM [U-95% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM tcep, 2 mM IP6, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM [U-95% 13C; U-95% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM tcep, 2 mM IP6, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6CUS HADDOCK structure of the Rous sarcoma virus matrix protein (M-domain) in complex with myo-inositol hexakisphosphate Deposited 2018-03-26 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–87（87 aa）
Mutation：M1S IHP INOSITOL HEXAKISPHOSPHATE × 1 SOLUTION NMR
NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 500 uM [U-98% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 2 mM INOSITOL HEXAKISPHOSPHATE, 95% H2O/5% D2O | 95% H2O/5% D2O
NMR sample composition 0.5 mM [U-98% 13C] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 2 mM INOSITOL HEXAKISPHOSPHATE, 100% D2O | 100% D2O
Resolution not provided
6CV8 HADDOCK structure of the Rous sarcoma virus matrix protein (M-domain) in complex with inositol 1,4,5-trisphosphate Deposited 2018-03-27 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–87（87 aa）
Mutation：M1S I3P D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE × 1 SOLUTION NMR
NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 100 uM [U-98% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 1.6 mM D-MYO-INOSITOL-1,4,5-TRIPHOSPHATE, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
6CW4 HADDOCK structure of the Rous sarcoma virus matrix protein (M-domain) in complex with inositol 1,3,5-trisphosphate Deposited 2018-03-29 Different construct Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–87（87 aa） Fragment：residues 1-87
Mutation：M1S FGV (1R,2S,3r,4R,5S,6s)-2,4,6-trihydroxycyclohexane-1,3,5-triyl tris[dihydrogen (phosphate)] × 1 SOLUTION NMR
NMR measurement conditions pH 6；305 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 100 uM [U-98% 15N] Matrix protein, 50 mM sodium phosphate, 2 mM TCEP, 1.6 mM IP3, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
7JN3 Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048 Deposited 2020-08-03 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 Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain B 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain C 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain D 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain E 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain F 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain G 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain H 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Not recorded ZN ZINC ION × 2 ZZX (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide × 2 MG MAGNESIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.21 Å
7KU7 Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. Cluster identified by 3-dimensional variability analysis in cryoSPARC. Deposited 2020-11-24 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 Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1281–1558（278 aa）
Chain B 1281–1558（278 aa）
Chain C 1281–1558（278 aa）
Chain D 1281–1558（278 aa）
Chain E 1281–1558（278 aa）
Chain F 1281–1558（278 aa）
Chain G 1281–1558（278 aa）
Chain H 1281–1558（278 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 4 ZZX (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7KUI Cryo-EM structure of Rous sarcoma virus cleaved synaptic complex (CSC) with HIV-1 integrase strand transfer inhibitor MK-2048. CIC region of a cluster identified by 3-dimensional variability analysis in cryoSPARC. Deposited 2020-11-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Homooligomer；Protein × 8 PDB declaration: dodecameric
Chain A 1281–1558（278 aa）
Chain B 1281–1558（278 aa）
Chain C 1281–1558（278 aa）
Chain D 1281–1558（278 aa）
Chain E 1281–1558（278 aa）
Chain F 1281–1558（278 aa）
Chain G 1281–1558（278 aa）
Chain H 1281–1558（278 aa）
Not recorded ZN ZINC ION × 2 ZZX (6S)-2-(3-chloro-4-fluorobenzyl)-8-ethyl-10-hydroxy-N,6-dimethyl-1,9-dioxo-1,2,6,7,8,9-hexahydropyrazino[1',2':1,5]pyrrolo[2,3-d]pyridazine-4-carboxamide × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8E14 Cryo-EM structure of Rous sarcoma virus strand transfer complex Deposited 2022-08-09 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 Homooligomer；Protein × 8 PDB declaration: tetradecameric
Chain A 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain B 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain C 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain D 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain E 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain F 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain G 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Chain H 1281–1558（278 aa） Fragment：UNP residues 1281-1558
Not recorded ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.36 Å

36 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name POL_RSVP
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 2–87； UniProt 2–87

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

SAXS profile for 6ccj

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6ccj
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6ccj
Deposition date deposition_date2018-02-07
Structure title titleNMR structure of the Rous sarcoma virus matrix protein (M domain)
Keywords keywordsRSV, ASV, matrix, Gag, helix, VIRAL PROTEIN; VIRAL PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.56 Å
Radius of gyration Rg (electron density) rg_electron12.30 Å
Forward intensity I(0) i0435834000.00
Molecular weight molecular_weight183700.0 kDa
Excluded volume excluded_volume233430 ų
Envelope volume envelope_volume18765 ų
Hydration-shell volume shell_volume11660 ų
Envelope diameter envelope_diameter46.5 Å
Shell Rg shell_rg19.48 Å
Envelope Rg envelope_rg14.22 Å
Shape Rg shape_rg12.26 Å
Total Rg total_rg12.60 Å
Total atoms total_atoms26360
Residues n_residues1740
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax39.9 Å
Rg (real space) rg_real12.48 Å
Rg uncertainty (real space) rg_real_error0.31 Å
I(0) (real space) i0_real4.3580e+08
I(0) uncertainty (real space) i0_real_error4.7980e+06
Rg (reciprocal space) rg_reciprocal12.48 Å
I(0) (reciprocal space) i0_reciprocal435800000.0000
Solution quality estimate total_estimate0.8830
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.9 Å
Skewness Skewness skewness0.006
Kurtosis Kurtosis kurtosis-0.413
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha82500.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.836; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.979
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6ccja1
Class classa — All alpha proteins
Fold Fold folda.61 — Retroviral matrix proteins
Superfamily Superfamily superfamilya.61.1 — Retroviral matrix proteins
Family Family familya.61.1.4 — GAG polyprotein M-domain
Domain ID domain_idd6ccja2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
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8. Citations (1)

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9. Files and Curves (10)