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- PDB-4mth: Crystal structure of mature human RegIIIalpha -

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Basic information

Entry
Database: PDB / ID: 4mth
TitleCrystal structure of mature human RegIIIalpha
ComponentsRegenerating islet-derived protein 3-alpha 15 kDa form
KeywordsANTIMICROBIAL PROTEIN / HIP/PAP / REGIII-GAMMA / C-TYPE LECTIN
Function / homology
Function and homology information


disruption of cell wall in another organism / positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Antimicrobial peptides ...disruption of cell wall in another organism / positive regulation of detection of glucose / response to symbiotic bacterium / positive regulation of keratinocyte proliferation / negative regulation of keratinocyte differentiation / negative regulation of inflammatory response to wounding / oligosaccharide binding / peptidoglycan binding / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Antimicrobial peptides / positive regulation of wound healing / acute-phase response / hormone activity / response to peptide hormone / response to wounding / negative regulation of inflammatory response / antimicrobial humoral immune response mediated by antimicrobial peptide / signaling receptor activity / carbohydrate binding / positive regulation of cell population proliferation / extracellular space / extracellular region / identical protein binding / cytoplasm
Similarity search - Function
C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold ...C-type lectin, conserved site / C-type lectin domain signature. / Mannose-Binding Protein A; Chain A / Mannose-Binding Protein A, subunit A / Lectin C-type domain / C-type lectin domain profile. / C-type lectin-like / C-type lectin (CTL) or carbohydrate-recognition domain (CRD) / C-type lectin-like/link domain superfamily / C-type lectin fold / Roll / Alpha Beta
Similarity search - Domain/homology
Regenerating islet-derived protein 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.47 Å
AuthorsDerebe, M.G.
CitationJournal: Nature / Year: 2014
Title: Antibacterial membrane attack by a pore-forming intestinal C-type lectin.
Authors: Sohini Mukherjee / Hui Zheng / Mehabaw G Derebe / Keith M Callenberg / Carrie L Partch / Darcy Rollins / Daniel C Propheter / Josep Rizo / Michael Grabe / Qiu-Xing Jiang / Lora V Hooper /
Abstract: Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are ...Human body-surface epithelia coexist in close association with complex bacterial communities and are protected by a variety of antibacterial proteins. C-type lectins of the RegIII family are bactericidal proteins that limit direct contact between bacteria and the intestinal epithelium and thus promote tolerance to the intestinal microbiota. RegIII lectins recognize their bacterial targets by binding peptidoglycan carbohydrate, but the mechanism by which they kill bacteria is unknown. Here we elucidate the mechanistic basis for RegIII bactericidal activity. We show that human RegIIIα (also known as HIP/PAP) binds membrane phospholipids and kills bacteria by forming a hexameric membrane-permeabilizing oligomeric pore. We derive a three-dimensional model of the RegIIIα pore by docking the RegIIIα crystal structure into a cryo-electron microscopic map of the pore complex, and show that the model accords with experimentally determined properties of the pore. Lipopolysaccharide inhibits RegIIIα pore-forming activity, explaining why RegIIIα is bactericidal for Gram-positive but not Gram-negative bacteria. Our findings identify C-type lectins as mediators of membrane attack in the mucosal immune system, and provide detailed insight into an antibacterial mechanism that promotes mutualism with the resident microbiota.
History
DepositionSep 19, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Regenerating islet-derived protein 3-alpha 15 kDa form
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6164
Polymers15,4201
Non-polymers1963
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.762, 49.528, 92.152
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Regenerating islet-derived protein 3-alpha 15 kDa form / REG-3-alpha / Hepatointestinal pancreatic protein / HIP/PAP / Human proislet peptide / Pancreatitis- ...REG-3-alpha / Hepatointestinal pancreatic protein / HIP/PAP / Human proislet peptide / Pancreatitis-associated protein 1 / Regenerating islet-derived protein III-alpha / Reg III-alpha


Mass: 15420.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIP, PAP, PAP1, REG3A / Plasmid: PET 3(A) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-RIPL / References: UniProt: Q06141
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.28 Å3/Da / Density % sol: 45.96 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 22% PEG 8000, 0.1M MES pH 6.0, 0.1M NACL, 10MM NAAC, 5% GLYCEROL, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 19, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.47→50 Å / Num. all: 24610 / Num. obs: 24610 / Biso Wilson estimate: 15.08 Å2 / Net I/σ(I): 2.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIX1.6.1_357refinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.47→26.13 Å / Occupancy max: 1 / Occupancy min: 0.47 / SU ML: 0.17 / σ(F): 0.13 / Phase error: 18.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.21 1876 8.1 %
Rwork0.185 --
obs0.187 23163 93.8 %
all-24610 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.14 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 58.44 Å2 / Biso mean: 20.7654 Å2 / Biso min: 7.97 Å2
Baniso -1Baniso -2Baniso -3
1--3.0153 Å20 Å2-0 Å2
2--3.4974 Å20 Å2
3----0.4821 Å2
Refinement stepCycle: LAST / Resolution: 1.47→26.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1084 0 3 181 1268
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONf_bond_d0.006
X-RAY DIFFRACTIONf_angle_deg1.029
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.471-1.52310.26211590.21851802196181
1.5231-1.58410.23851690.19651978214788
1.5841-1.65620.21671740.18511998217290
1.6562-1.74350.23171830.17192058224192
1.7435-1.85270.18981840.1772113229795
1.8527-1.99570.2071910.16532162235396
1.9957-2.19640.19152010.16932236243799
2.1964-2.5140.20192000.18992236243698
2.514-3.16650.22752010.18842290249199
3.1665-26.13590.19982140.1832414262899

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