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- PDB-7pdc: The structure of the human tetrameric LL-37 peptide in a channel ... -

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Basic information

Entry
Database: PDB / ID: 7pdc
TitleThe structure of the human tetrameric LL-37 peptide in a channel conformation
ComponentsCathelicidin antimicrobial peptide
KeywordsANTIMICROBIAL PROTEIN / Antimicrobial peptide / LL-37 / channel
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 / Resolution: 1.83 Å
AuthorsZeth, K. / Sancho-Vaello, E.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Sci Rep / Year: 2020
Title: The structure of the antimicrobial human cathelicidin LL-37 shows oligomerization and channel formation in the presence of membrane mimics.
Authors: Sancho-Vaello, E. / Gil-Carton, D. / Francois, P. / Bonetti, E.J. / Kreir, M. / Pothula, K.R. / Kleinekathofer, U. / Zeth, K.
History
DepositionAug 5, 2021Deposition site: PDBE / Processing site: PDBE
SupersessionSep 8, 2021ID: 5G1J
Revision 1.0Sep 8, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 3, 2021Group: Data collection / Category: pdbx_depui_entry_details / Item: _pdbx_depui_entry_details.replace_pdb_id
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)9,0443
Polymers9,0092
Non-polymers351
Water18010
1
A: Cathelicidin antimicrobial peptide
B: Cathelicidin antimicrobial peptide
hetero molecules

A: Cathelicidin antimicrobial peptide
B: Cathelicidin antimicrobial peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,0886
Polymers18,0174
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area3890 Å2
ΔGint-18 kcal/mol
Surface area9480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.100, 51.420, 26.220
Angle α, β, γ (deg.)90.00, 106.36, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-101-

CL

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Components

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


Mass: 4504.351 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: LLGDFFRKSKEKIGKEFKRIVQRIKDFLRNLVPRTES / Source: (gene. exp.) Homo sapiens (human) / Gene: CAMP, CAP18, FALL39, HSD26 / Production host: chemical production metagenome (others) / References: UniProt: P49913
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.91 Å3/Da / Density % sol: 35.48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 20% PEG 20K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 15, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.83→50 Å / Num. obs: 5827 / % possible obs: 96.7 % / Redundancy: 3.2 % / Biso Wilson estimate: 41.96 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.11 / Net I/σ(I): 5.38
Reflection shellResolution: 1.83→1.94 Å / Rmerge(I) obs: 1.29 / Mean I/σ(I) obs: 0.84 / Num. unique obs: 500 / CC1/2: 0.19

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Processing

Software
NameVersionClassification
BUSTER2.10.0refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5NNM

5nnm


Resolution: 1.83→36.19 Å / Cor.coef. Fo:Fc: 0.9309 / Cor.coef. Fo:Fc free: 0.9117 / SU R Cruickshank DPI: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.166 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.167
RfactorNum. reflection% reflectionSelection details
Rfree0.3023 562 9.64 %RANDOM
Rwork0.2518 ---
obs0.2566 5827 96.6 %-
Displacement parametersBiso mean: 54.05 Å2
Baniso -1Baniso -2Baniso -3
1-1.6985 Å20 Å21.6594 Å2
2---7.0235 Å20 Å2
3---5.325 Å2
Refine analyzeLuzzati coordinate error obs: 0.268 Å
Refinement stepCycle: LAST / Resolution: 1.83→36.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms498 0 1 10 509
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.01516HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.96676HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d221SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes11HARMONIC2
X-RAY DIFFRACTIONt_gen_planes75HARMONIC5
X-RAY DIFFRACTIONt_it516HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.12
X-RAY DIFFRACTIONt_other_torsion18.33
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion62SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact568SEMIHARMONIC4
LS refinement shellResolution: 1.83→2.05 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2405 145 9.28 %
Rwork0.2242 1417 -
all0.2257 1562 -
obs--96.6 %

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