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- PDB-6s6m: Crystal structure of the human LL37(17-29) antimicrobial peptide -

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Basic information

Entry
Database: PDB / ID: 6s6m
TitleCrystal structure of the human LL37(17-29) antimicrobial peptide
ComponentsCathelicidin antimicrobial peptide
KeywordsPROTEIN FIBRIL / Helical and tubular fibril structure of a human derived antimicrobial peptide
Function / homology
Function and homology information


cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection ...cytolysis / killing by host of symbiont cells / neutrophil activation / specific granule / cellular response to peptidoglycan / cellular response to interleukin-6 / Antimicrobial peptides / cellular response to interleukin-1 / innate immune response in mucosa / cell projection / lipopolysaccharide binding / specific granule lumen / positive regulation of angiogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / tertiary granule lumen / cellular response to tumor necrosis factor / antibacterial humoral response / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / amyloid fibril formation / defense response to Gram-positive bacterium / defense response to bacterium / positive regulation of protein phosphorylation / innate immune response / positive regulation of cell population proliferation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region
Similarity search - Function
Cathelicidin, antimicrobial peptide, C-terminal / LPS binding domain of CAP18 (C terminal) / Cathelicidin / Cathelicidins signature 1. / Cathelicidin, conserved site / Cathelicidins signature 2. / Cathelicidin-like / Cystatin superfamily
Similarity search - Domain/homology
Cathelicidin antimicrobial peptide
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
Model detailsAntimicrobial
AuthorsLandau, M. / Engelberg, Y.
CitationJournal: Nat Commun / Year: 2020
Title: The Human LL-37(17-29) antimicrobial peptide reveals a functional supramolecular structure.
Authors: Engelberg, Y. / Landau, M.
History
DepositionJul 3, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cathelicidin antimicrobial peptide
B: Cathelicidin antimicrobial peptide


Theoretical massNumber of molelcules
Total (without water)3,4482
Polymers3,4482
Non-polymers00
Water55831
1
A: Cathelicidin antimicrobial peptide
x 165
B: Cathelicidin antimicrobial peptide
x 175


Theoretical massNumber of molelcules
Total (without water)586,203340
Polymers586,203340
Non-polymers00
Water6,125340
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
crystal symmetry operation1_554x,y,z-12
crystal symmetry operation1_553x,y,z-22
crystal symmetry operation1_552x,y,z-32
crystal symmetry operation1_551x,y,z-42
crystal symmetry operation1_545x,y-1,z2
crystal symmetry operation1_544x,y-1,z-12
crystal symmetry operation1_543x,y-1,z-22
crystal symmetry operation1_542x,y-1,z-32
crystal symmetry operation1_541x,y-1,z-42
crystal symmetry operation1_655x+1,y,z1
crystal symmetry operation1_654x+1,y,z-11
crystal symmetry operation1_653x+1,y,z-21
crystal symmetry operation1_652x+1,y,z-31
crystal symmetry operation1_651x+1,y,z-41
crystal symmetry operation2_555-y,x-y,z+1/32
crystal symmetry operation2_554-y,x-y,z-2/32
crystal symmetry operation2_553-y,x-y,z-5/32
crystal symmetry operation2_552-y,x-y,z-8/32
crystal symmetry operation2_551-y,x-y,z-11/32
crystal symmetry operation2_665-y+1,x-y+1,z+1/32
crystal symmetry operation2_664-y+1,x-y+1,z-2/32
crystal symmetry operation2_663-y+1,x-y+1,z-5/32
crystal symmetry operation2_662-y+1,x-y+1,z-8/32
crystal symmetry operation2_661-y+1,x-y+1,z-11/32
crystal symmetry operation2_565-y,x-y+1,z+1/31
crystal symmetry operation2_564-y,x-y+1,z-2/31
crystal symmetry operation2_563-y,x-y+1,z-5/31
crystal symmetry operation2_562-y,x-y+1,z-8/31
crystal symmetry operation2_561-y,x-y+1,z-11/31
crystal symmetry operation3_555-x+y,-x,z+2/32
crystal symmetry operation3_554-x+y,-x,z-1/32
crystal symmetry operation3_553-x+y,-x,z-4/32
crystal symmetry operation3_552-x+y,-x,z-7/32
crystal symmetry operation3_551-x+y,-x,z-10/32
crystal symmetry operation3_455-x+y-1,-x,z+2/32
crystal symmetry operation3_454-x+y-1,-x,z-1/32
crystal symmetry operation3_453-x+y-1,-x,z-4/32
crystal symmetry operation3_452-x+y-1,-x,z-7/32
crystal symmetry operation3_451-x+y-1,-x,z-10/32
crystal symmetry operation4_555-x,-y,z+1/22
crystal symmetry operation4_554-x,-y,z-1/22
crystal symmetry operation4_553-x,-y,z-3/22
crystal symmetry operation4_552-x,-y,z-5/22
crystal symmetry operation4_551-x,-y,z-7/22
crystal symmetry operation4_455-x-1,-y,z+1/21
crystal symmetry operation4_454-x-1,-y,z-1/21
crystal symmetry operation4_453-x-1,-y,z-3/21
crystal symmetry operation4_452-x-1,-y,z-5/21
crystal symmetry operation4_451-x-1,-y,z-7/21
crystal symmetry operation5_555y,-x+y,z+5/62
crystal symmetry operation5_554y,-x+y,z-1/62
crystal symmetry operation5_553y,-x+y,z-7/62
crystal symmetry operation5_552y,-x+y,z-13/62
crystal symmetry operation5_551y,-x+y,z-19/62
crystal symmetry operation5_445y-1,-x+y-1,z+5/62
crystal symmetry operation5_444y-1,-x+y-1,z-1/62
crystal symmetry operation5_443y-1,-x+y-1,z-7/62
crystal symmetry operation5_442y-1,-x+y-1,z-13/62
crystal symmetry operation5_441y-1,-x+y-1,z-19/62
crystal symmetry operation5_545y,-x+y-1,z+5/61
crystal symmetry operation5_544y,-x+y-1,z-1/61
crystal symmetry operation5_543y,-x+y-1,z-7/61
crystal symmetry operation5_542y,-x+y-1,z-13/61
crystal symmetry operation5_541y,-x+y-1,z-19/61
crystal symmetry operation6_555x-y,x,z+1/62
crystal symmetry operation6_554x-y,x,z-5/62
crystal symmetry operation6_553x-y,x,z-11/62
crystal symmetry operation6_552x-y,x,z-17/62
crystal symmetry operation6_551x-y,x,z-23/62
crystal symmetry operation6_655x-y+1,x,z+1/62
crystal symmetry operation6_654x-y+1,x,z-5/62
crystal symmetry operation6_653x-y+1,x,z-11/62
crystal symmetry operation6_652x-y+1,x,z-17/62
crystal symmetry operation6_651x-y+1,x,z-23/62
crystal symmetry operation6_665x-y+1,x+1,z+1/61
crystal symmetry operation6_664x-y+1,x+1,z-5/61
crystal symmetry operation6_663x-y+1,x+1,z-11/61
crystal symmetry operation6_662x-y+1,x+1,z-17/61
crystal symmetry operation6_661x-y+1,x+1,z-23/61
crystal symmetry operation7_555y,x,-z+1/32
crystal symmetry operation7_554y,x,-z-2/32
crystal symmetry operation7_553y,x,-z-5/32
crystal symmetry operation7_552y,x,-z-8/32
crystal symmetry operation7_551y,x,-z-11/32
crystal symmetry operation7_455y-1,x,-z+1/32
crystal symmetry operation7_454y-1,x,-z-2/32
crystal symmetry operation7_453y-1,x,-z-5/32
crystal symmetry operation7_452y-1,x,-z-8/32
crystal symmetry operation7_451y-1,x,-z-11/32
crystal symmetry operation7_565y,x+1,-z+1/31
crystal symmetry operation7_564y,x+1,-z-2/31
crystal symmetry operation7_563y,x+1,-z-5/31
crystal symmetry operation7_562y,x+1,-z-8/31
crystal symmetry operation7_561y,x+1,-z-11/31
crystal symmetry operation8_555x-y,-y,-z2
crystal symmetry operation8_554x-y,-y,-z-12
crystal symmetry operation8_553x-y,-y,-z-22
crystal symmetry operation8_552x-y,-y,-z-32
crystal symmetry operation8_551x-y,-y,-z-42
crystal symmetry operation8_665x-y+1,-y+1,-z2
crystal symmetry operation8_664x-y+1,-y+1,-z-12
crystal symmetry operation8_663x-y+1,-y+1,-z-22
crystal symmetry operation8_662x-y+1,-y+1,-z-32
crystal symmetry operation8_661x-y+1,-y+1,-z-42
crystal symmetry operation8_655x-y+1,-y,-z1
crystal symmetry operation8_654x-y+1,-y,-z-11
crystal symmetry operation8_653x-y+1,-y,-z-21
crystal symmetry operation8_652x-y+1,-y,-z-31
crystal symmetry operation8_651x-y+1,-y,-z-41
crystal symmetry operation9_555-x,-x+y,-z+2/32
crystal symmetry operation9_554-x,-x+y,-z-1/32
crystal symmetry operation9_553-x,-x+y,-z-4/32
crystal symmetry operation9_552-x,-x+y,-z-7/32
crystal symmetry operation9_551-x,-x+y,-z-10/32
crystal symmetry operation9_545-x,-x+y-1,-z+2/32
crystal symmetry operation9_544-x,-x+y-1,-z-1/32
crystal symmetry operation9_543-x,-x+y-1,-z-4/32
crystal symmetry operation9_542-x,-x+y-1,-z-7/32
crystal symmetry operation9_541-x,-x+y-1,-z-10/32
crystal symmetry operation9_445-x-1,-x+y-1,-z+2/31
crystal symmetry operation9_444-x-1,-x+y-1,-z-1/31
crystal symmetry operation9_443-x-1,-x+y-1,-z-4/31
crystal symmetry operation9_442-x-1,-x+y-1,-z-7/31
crystal symmetry operation9_441-x-1,-x+y-1,-z-10/31
crystal symmetry operation10_555-y,-x,-z+5/62
crystal symmetry operation10_554-y,-x,-z-1/62
crystal symmetry operation10_553-y,-x,-z-7/62
crystal symmetry operation10_552-y,-x,-z-13/62
crystal symmetry operation10_551-y,-x,-z-19/62
crystal symmetry operation10_655-y+1,-x,-z+5/62
crystal symmetry operation10_654-y+1,-x,-z-1/62
crystal symmetry operation10_653-y+1,-x,-z-7/62
crystal symmetry operation10_652-y+1,-x,-z-13/62
crystal symmetry operation10_651-y+1,-x,-z-19/62
crystal symmetry operation11_555-x+y,y,-z+1/22
crystal symmetry operation11_554-x+y,y,-z-1/22
crystal symmetry operation11_553-x+y,y,-z-3/22
crystal symmetry operation11_552-x+y,y,-z-5/22
crystal symmetry operation11_551-x+y,y,-z-7/22
crystal symmetry operation11_445-x+y-1,y-1,-z+1/22
crystal symmetry operation11_444-x+y-1,y-1,-z-1/22
crystal symmetry operation11_443-x+y-1,y-1,-z-3/22
crystal symmetry operation11_442-x+y-1,y-1,-z-5/22
crystal symmetry operation11_441-x+y-1,y-1,-z-7/22
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation11_454-x+y-1,y,-z-1/21
crystal symmetry operation11_453-x+y-1,y,-z-3/21
crystal symmetry operation11_452-x+y-1,y,-z-5/21
crystal symmetry operation11_451-x+y-1,y,-z-7/21
crystal symmetry operation12_555x,x-y,-z+1/62
crystal symmetry operation12_554x,x-y,-z-5/62
crystal symmetry operation12_553x,x-y,-z-11/62
crystal symmetry operation12_552x,x-y,-z-17/62
crystal symmetry operation12_551x,x-y,-z-23/62
crystal symmetry operation12_565x,x-y+1,-z+1/62
crystal symmetry operation12_564x,x-y+1,-z-5/62
crystal symmetry operation12_563x,x-y+1,-z-11/62
crystal symmetry operation12_562x,x-y+1,-z-17/62
crystal symmetry operation12_561x,x-y+1,-z-23/62
crystal symmetry operation12_665x+1,x-y+1,-z+1/61
crystal symmetry operation12_664x+1,x-y+1,-z-5/61
crystal symmetry operation12_663x+1,x-y+1,-z-11/61
crystal symmetry operation12_662x+1,x-y+1,-z-17/61
crystal symmetry operation12_661x+1,x-y+1,-z-23/61
crystal symmetry operation1_445x-1,y-1,z1
crystal symmetry operation1_444x-1,y-1,z-11
crystal symmetry operation1_443x-1,y-1,z-21
crystal symmetry operation1_442x-1,y-1,z-31
crystal symmetry operation1_441x-1,y-1,z-41
crystal symmetry operation2_655-y+1,x-y,z+1/31
crystal symmetry operation2_654-y+1,x-y,z-2/31
crystal symmetry operation2_653-y+1,x-y,z-5/31
crystal symmetry operation2_652-y+1,x-y,z-8/31
crystal symmetry operation2_651-y+1,x-y,z-11/31
crystal symmetry operation3_565-x+y,-x+1,z+2/31
crystal symmetry operation3_564-x+y,-x+1,z-1/31
crystal symmetry operation3_563-x+y,-x+1,z-4/31
crystal symmetry operation3_562-x+y,-x+1,z-7/31
crystal symmetry operation3_561-x+y,-x+1,z-10/31
crystal symmetry operation4_665-x+1,-y+1,z+1/21
crystal symmetry operation4_664-x+1,-y+1,z-1/21
crystal symmetry operation4_663-x+1,-y+1,z-3/21
crystal symmetry operation4_662-x+1,-y+1,z-5/21
crystal symmetry operation4_661-x+1,-y+1,z-7/21
crystal symmetry operation5_455y-1,-x+y,z+5/61
crystal symmetry operation5_454y-1,-x+y,z-1/61
crystal symmetry operation5_453y-1,-x+y,z-7/61
crystal symmetry operation5_452y-1,-x+y,z-13/61
crystal symmetry operation5_451y-1,-x+y,z-19/61
crystal symmetry operation6_545x-y,x-1,z+1/61
crystal symmetry operation6_544x-y,x-1,z-5/61
crystal symmetry operation6_543x-y,x-1,z-11/61
crystal symmetry operation6_542x-y,x-1,z-17/61
crystal symmetry operation6_541x-y,x-1,z-23/61
crystal symmetry operation7_445y-1,x-1,-z+1/31
crystal symmetry operation7_444y-1,x-1,-z-2/31
crystal symmetry operation7_443y-1,x-1,-z-5/31
crystal symmetry operation7_442y-1,x-1,-z-8/31
crystal symmetry operation7_441y-1,x-1,-z-11/31
crystal symmetry operation8_565x-y,-y+1,-z1
crystal symmetry operation8_564x-y,-y+1,-z-11
crystal symmetry operation8_563x-y,-y+1,-z-21
crystal symmetry operation8_562x-y,-y+1,-z-31
crystal symmetry operation8_561x-y,-y+1,-z-41
crystal symmetry operation9_655-x+1,-x+y,-z+2/31
crystal symmetry operation9_654-x+1,-x+y,-z-1/31
crystal symmetry operation9_653-x+1,-x+y,-z-4/31
crystal symmetry operation9_652-x+1,-x+y,-z-7/31
crystal symmetry operation9_651-x+1,-x+y,-z-10/31
crystal symmetry operation10_665-y+1,-x+1,-z+5/61
crystal symmetry operation10_664-y+1,-x+1,-z-1/61
crystal symmetry operation10_663-y+1,-x+1,-z-7/61
crystal symmetry operation10_662-y+1,-x+1,-z-13/61
crystal symmetry operation10_661-y+1,-x+1,-z-19/61
crystal symmetry operation11_545-x+y,y-1,-z+1/21
crystal symmetry operation11_544-x+y,y-1,-z-1/21
crystal symmetry operation11_543-x+y,y-1,-z-3/21
crystal symmetry operation11_542-x+y,y-1,-z-5/21
crystal symmetry operation11_541-x+y,y-1,-z-7/21
crystal symmetry operation12_455x-1,x-y,-z+1/61
crystal symmetry operation12_454x-1,x-y,-z-5/61
crystal symmetry operation12_453x-1,x-y,-z-11/61
crystal symmetry operation12_452x-1,x-y,-z-17/61
crystal symmetry operation12_451x-1,x-y,-z-23/61
Unit cell
Length a, b, c (Å)41.450, 41.450, 57.470
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-102-

HOH

21A-115-

HOH

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Components

#1: Protein/peptide Cathelicidin antimicrobial peptide / 18 kDa cationic antimicrobial protein / hCAP-18


Mass: 1724.125 Da / Num. of mol.: 2
Fragment: Antimicrobial core segment of human LL37 (residues 17-29)
Source method: obtained synthetically / Details: Human LL37(17-29), synthesized / Source: (synth.) Homo sapiens (human) / References: UniProt: P49913
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: Reservoir contained 0.2 M Sodium Acetate, 0.1 M TRIS pH 8.5, 30 %w/v PEG 4K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 7, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.35→19.5 Å / Num. obs: 6782 / % possible obs: 98.7 % / Redundancy: 8.82 % / Biso Wilson estimate: 21.958 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.06 / Χ2: 0.994 / Net I/σ(I): 21.46 / Num. measured all: 59815 / Scaling rejects: 176
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
1.35-1.398.8510.7883.5344705065050.8970.83999.8
1.39-1.429.0530.714.5342644734710.9250.75499.6
1.42-1.468.6870.6585.8139354554530.90.70199.6
1.46-1.518.8630.4887.940684644590.9660.51898.9
1.51-1.569.3660.29911.1340744354350.9770.316100
1.56-1.619.4350.18414.2240954354340.990.19499.8
1.61-1.679.4830.14916.1838884104100.9940.157100
1.67-1.749.1480.13217.3236594014000.9930.1499.8
1.74-1.829.3290.09920.8135453813800.9970.10599.7
1.82-1.918.4480.09422.7630333743590.9960.196
1.91-2.017.7910.0827.5125713483300.9950.08594.8
2.01-2.138.6960.05733.0329743423420.9980.061100
2.13-2.288.1750.05436.4224693143020.9980.05896.2
2.28-2.469.1980.04540.3727413012980.9980.04899
2.46-2.79.2030.04242.725402762760.9990.044100
2.7-3.028.6590.03842.8822342582580.9990.041100
3.02-3.498.4650.03643.9419302312280.9990.03898.7
3.49-4.277.8320.03843.5414881991900.9950.04195.5
4.27-6.047.9940.03842.9912791651600.9960.04197
6.04-19.56.0650.03235.67558106920.9970.03786.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0253refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.35→19.5 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.909 / SU B: 1.185 / SU ML: 0.048 / SU R Cruickshank DPI: 0.0806 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.083
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2679 679 10 %RANDOM
Rwork0.2321 ---
obs0.2357 6103 98.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 47.68 Å2 / Biso mean: 16.795 Å2 / Biso min: 10.04 Å2
Baniso -1Baniso -2Baniso -3
1--0.16 Å2-0.08 Å20 Å2
2---0.16 Å20 Å2
3---0.52 Å2
Refinement stepCycle: final / Resolution: 1.35→19.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms244 0 0 31 275
Biso mean---28.26 -
Num. residues----26
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.013275
X-RAY DIFFRACTIONr_bond_other_d0.030.017306
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.695366
X-RAY DIFFRACTIONr_angle_other_deg1.3771.634700
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.465530
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.28816.66724
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2641568
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.379157
X-RAY DIFFRACTIONr_chiral_restr0.0720.234
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.02306
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0283
LS refinement shellResolution: 1.35→1.385 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 51 -
Rwork0.399 452 -
all-503 -
obs--99.8 %

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