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- PDB-5hcp: Crystal structure of antimicrobial peptide Metalnikowin bound to ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5hcp | ||||||||||||
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Title | Crystal structure of antimicrobial peptide Metalnikowin bound to the Thermus thermophilus 70S ribosome | ||||||||||||
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![]() | Ribosome/Antibiotic / Metalnikowin / antimicrobial peptide / antibiotic / 70S ribosome / inhibition of translation / peptidyl transferase inhibitors / 50S ribosomal subunit / peptide exit tunnel / Ribosome-Antibiotic Complex | ||||||||||||
Function / homology | ![]() large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium ...large ribosomal subunit / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / innate immune response / mRNA binding / zinc ion binding / extracellular region / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Gagnon, M.G. / Roy, R.N. / Lomakin, I.B. / Florin, T. / Mankin, A.S. / Steitz, T.A. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Structures of proline-rich peptides bound to the ribosome reveal a common mechanism of protein synthesis inhibition. Authors: Gagnon, M.G. / Roy, R.N. / Lomakin, I.B. / Florin, T. / Mankin, A.S. / Steitz, T.A. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 7.4 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 622.9 KB | Display | |
Data in CIF | ![]() | 987.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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Components
-RNA chain , 5 types, 10 molecules 1A2A1B2B1a2a1v2v1x2x
#1: RNA chain | Mass: 947895.375 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #2: RNA chain | Mass: 39188.371 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #32: RNA chain | Mass: 493652.156 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #53: RNA chain | Mass: 7804.735 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: IDT-Synthesized 24-nt M-F-Stop mRNA / Source: (synth.) ![]() #54: RNA chain | Mass: 24846.902 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: Initiator Methionine tRNA / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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+50S ribosomal protein ... , 29 types, 58 molecules 1D2D1E2E1F2F1G2G1H2H1I2I1N2N1O2O1P2P1Q2Q1R2R1S2S1T2T1U2U1V2V...
-30S ribosomal protein ... , 20 types, 40 molecules 1b2b1c2c1d2d1e2e1f2f1g2g1h2h1i2i1j2j1k2k1l2l1m2m1n2n1o2o1p2p...
#33: Protein | Mass: 29317.703 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80371 #34: Protein | Mass: 26751.076 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80372 #35: Protein | Mass: 24373.447 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80373 #36: Protein | Mass: 17583.416 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ5 #37: Protein | Mass: 11988.753 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLP8 #38: Protein | Mass: 18050.973 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P17291 #39: Protein | Mass: 15868.570 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ2, UniProt: A0A0M9AFS9*PLUS #40: Protein | Mass: 14410.614 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80374 #41: Protein | Mass: 11954.968 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN7 #42: Protein | Mass: 13737.868 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80376 #43: Protein | Mass: 14637.384 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHN3 #44: Protein | Mass: 14338.861 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80377 #45: Protein | Mass: 7158.725 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHQ1, UniProt: A0A0N0BLP2*PLUS #46: Protein | Mass: 10578.407 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJ76 #47: Protein | Mass: 10409.983 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SJH3 #48: Protein | Mass: 12325.655 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP7, UniProt: A0A0N0BLS5*PLUS #49: Protein | Mass: 10258.299 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SLQ0 #50: Protein | Mass: 10605.464 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SHP2 #51: Protein | Mass: 11736.143 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: P80380 #52: Protein/peptide | Mass: 3350.030 Da / Num. of mol.: 2 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Strain: HB8 / ATCC 27634 / DSM 579 / References: UniProt: Q5SIH3 |
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-Protein/peptide , 1 types, 2 molecules 1z2z
#55: Protein/peptide | Mass: 1842.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Details: GenScript-Synthesized peptide Metalnikowin / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 6939 molecules ![](data/chem/img/MG.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/ZN.gif)
![](data/chem/img/SF4.gif)
![](data/chem/img/HOH.gif)
#56: Chemical | ChemComp-MG / #57: Chemical | ChemComp-ZN / #58: Chemical | #59: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.27 % / Description: Long needles |
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Crystal grow | Temperature: 292 K / Method: vapor diffusion Details: 0.15M Arginine-HCl, 0.1M Tris-HCl pH 7.3-7.6, 2.6-2.9% PEG-20K, 9-10% MPD, 0.5 mM BME PH range: 7.3-7.6 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 13, 2015 / Details: S/N 60-0112-F | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.89→50 Å / Num. all: 1296307 / Num. obs: 1277977 / % possible obs: 98.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): -3 / Redundancy: 4.891 % / Biso Wilson estimate: 56.91 Å2 / Rmerge F obs: 0.992 / Rmerge(I) obs: 0.216 / Rrim(I) all: 0.241 / Χ2: 1.106 / Net I/σ(I): 9.07 / Num. measured all: 6250510 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]()
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 152.75 Å2 / Biso mean: 59.41 Å2 / Biso min: 4.48 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.894→49.848 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30
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