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- PDB-9wtd: Filament structure of human Reg3alpha -

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Basic information

Entry
Database: PDB / ID: 9wtd
TitleFilament structure of human Reg3alpha
ComponentsRegenerating islet-derived protein 3-alpha 15 kDa form
KeywordsANTIMICROBIAL PROTEIN / C-type lectin domain containing protein / antimicrobial activity / cryo-EM / protein filament
Function / homology
Function and homology information


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 / Antimicrobial peptides / positive regulation of wound healing ...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 / Antimicrobial peptides / positive regulation of wound healing / acute-phase response / hormone activity / response to wounding / response to peptide hormone / 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. / 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
Similarity search - Domain/homology
Regenerating islet-derived protein 3-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.21 Å
AuthorsCao, Q. / Han, J.T.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32271276 China
CitationJournal: Commun Chem / Year: 2026
Title: Structural basis for human RegIIIalpha filament formation
Authors: Cao, Q. / Han, J.T.
History
DepositionSep 16, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Feb 11, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 11, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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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
B: Regenerating islet-derived protein 3-alpha 15 kDa form
D: Regenerating islet-derived protein 3-alpha 15 kDa form
E: Regenerating islet-derived protein 3-alpha 15 kDa form
F: Regenerating islet-derived protein 3-alpha 15 kDa form
G: Regenerating islet-derived protein 3-alpha 15 kDa form
H: Regenerating islet-derived protein 3-alpha 15 kDa form
I: Regenerating islet-derived protein 3-alpha 15 kDa form
J: Regenerating islet-derived protein 3-alpha 15 kDa form
K: Regenerating islet-derived protein 3-alpha 15 kDa form
L: Regenerating islet-derived protein 3-alpha 15 kDa form
C: Regenerating islet-derived protein 3-alpha 15 kDa form


Theoretical massNumber of molelcules
Total (without water)183,46912
Polymers183,46912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and (resid 38 through 98 or resid 100 through 175))
d_2ens_1(chain "B" and (resid 38 through 98 or resid 100 through 175))
d_3ens_1(chain "C" and (resid 38 through 98 or resid 100 through 175))
d_4ens_1(chain "D" and (resid 38 through 98 or resid 100 through 175))
d_5ens_1(chain "E" and (resid 38 through 98 or resid 100 through 175))
d_6ens_1(chain "F" and (resid 38 through 98 or resid 100 through 175))
d_7ens_1(chain "G" and (resid 38 through 98 or resid 100 through 175))
d_8ens_1(chain "H" and (resid 38 through 98 or resid 100 through 175))
d_9ens_1(chain "I" and (resid 38 through 98 or resid 100 through 175))
d_10ens_1(chain "J" and (resid 38 through 98 or resid 100 through 175))
d_11ens_1(chain "K" and (resid 38 through 98 or resid 100 through 175))
d_12ens_1(chain "L" and (resid 38 through 98 or resid 100 through 175))

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ILEILESERSERAA38 - 981 - 61
d_12SERSERASPASPAA100 - 17563 - 138
d_21ILEILESERSERBB38 - 981 - 61
d_22SERSERASPASPBB100 - 17563 - 138
d_31ILEILESERSERCL38 - 981 - 61
d_32SERSERASPASPCL100 - 17563 - 138
d_41ILEILESERSERDC38 - 981 - 61
d_42SERSERASPASPDC100 - 17563 - 138
d_51ILEILESERSERED38 - 981 - 61
d_52SERSERASPASPED100 - 17563 - 138
d_61ILEILESERSERFE38 - 981 - 61
d_62SERSERASPASPFE100 - 17563 - 138
d_71ILEILESERSERGF38 - 981 - 61
d_72SERSERASPASPGF100 - 17563 - 138
d_81ILEILESERSERHG38 - 981 - 61
d_82SERSERASPASPHG100 - 17563 - 138
d_91ILEILESERSERIH38 - 981 - 61
d_92SERSERASPASPIH100 - 17563 - 138
d_101ILEILESERSERJI38 - 981 - 61
d_102SERSERASPASPJI100 - 17563 - 138
d_111ILEILESERSERKJ38 - 981 - 61
d_112SERSERASPASPKJ100 - 17563 - 138
d_121ILEILESERSERLK38 - 981 - 61
d_122SERSERASPASPLK100 - 17563 - 138

NCS oper:
IDCodeMatrixVector
1given(0.583661312099, -0.811996805589, 0.000812693945668), (0.811996835903, 0.583661712887, 0.000378672920428), (-0.000781819542132, 0.000438888178847, 0.999999598068)205.920707611, -66.4367089864, 20.5232172755
2given(-0.320429903456, -0.947272059512, 0.000567661325299), (0.947267870597, -0.320426553455, 0.00322570543915), (-0.00287372687273, 0.00157133981728, 0.999994636278)380.342977938, 62.0015433528, 41.1843295924
3given(-0.955656890444, -0.294481495661, 0.000745962418746), (0.294481872783, -0.95565695598, 0.000457261700165), (0.000578229065002, 0.000656657704597, 0.999999617226)377.433762791, 278.578255928, 61.1681362049
4given(-0.505820019289, -0.862638852758, 0.000563736148143), (0.862638590035, -0.505818984001, 0.00134848305918), (-0.000878105433438, 0.00116839028299, 0.999998931897)397.252350308, 107.583276424, -0.054069605831
5given(-0.994932558231, -0.100542147685, -0.000693622202027), (0.100542414233, -0.994932707703, -0.000360671152367), (-0.000653844763319, -0.000428581923062, 0.999999694402)351.655621149, 317.849694694, 20.6385949336
6given(-0.656334527012, 0.754465459439, -0.00261900069842), (-0.754468524065, -0.656336162377, 0.000296904617085), (-0.00149494058932, 0.00217082234288, 0.999996526335)151.827714794, 404.463690038, 40.795702318
7given(0.221795768384, 0.97509295517, -0.000604901257378), (-0.975093119156, 0.221795583731, -0.000357787340266), (-0.000214711487463, 0.00066919077189, 0.999999753041)-32.9349083997, 294.236688312, 61.2950636709
8given(-0.495095263484, 0.868838616075, -0.000373219981486), (-0.868838643282, -0.495095037656, 0.000561808279161), (0.000303341366978, 0.000602416560359, 0.999999772539)105.243146999, 396.59669684, -0.167736536916
9given(0.411229209359, 0.911530200299, -0.00179758521683), (-0.911531679849, 0.411226696639, -0.00161263814845), (-0.000730753343818, 0.00230171978314, 0.999997084039)-53.912798197, 251.960806023, 20.2261595942
10given(0.979732895875, 0.200307983874, -0.000405383477343), (-0.200308388219, 0.979731350454, -0.00174084633285), (4.8461482542E-5, 0.00178676612991, 0.999998402558)-30.145319504, 37.2276117086, 40.6281601899
11given(0.73361943726, -0.679560354052, 0.000496462507208), (0.679560535398, 0.733619243454, -0.000533257503261), (-1.83379122449E-6, 0.000728584396661, 0.999999734581)158.568408281, -69.2676389463, 61.256884038

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Components

#1: Protein
Regenerating islet-derived protein 3-alpha 15 kDa form


Mass: 15289.049 Da / Num. of mol.: 12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: REG3A, HIP, PAP, PAP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q06141
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Filaments formed by regenerating islet-derived protein 3-alpha
Type: RIBOSOME / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARCV4.0.1particle selection
7UCSF ChimeraXmodel fitting
12cryoSPARCV4.0.13D reconstruction
13PHENIXmodel refinement
CTF correctionType: NONE
Helical symmertyAngular rotation/subunit: 54.24 ° / Axial rise/subunit: 20.47 Å / Axial symmetry: C3
Particle selectionNum. of particles selected: 802654
3D reconstructionResolution: 2.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 762506 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 51.72 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.001913452
ELECTRON MICROSCOPYf_angle_d0.44818336
ELECTRON MICROSCOPYf_chiral_restr0.03831872
ELECTRON MICROSCOPYf_plane_restr0.00342340
ELECTRON MICROSCOPYf_dihedral_angle_d4.40861848
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAELECTRON MICROSCOPYNCS constraints0.000712696596014
ens_1d_3AAELECTRON MICROSCOPYNCS constraints0.000714526731085
ens_1d_4AAELECTRON MICROSCOPYNCS constraints0.000712536936149
ens_1d_5AAELECTRON MICROSCOPYNCS constraints0.000700728391439
ens_1d_6AAELECTRON MICROSCOPYNCS constraints0.000717436276085
ens_1d_7AAELECTRON MICROSCOPYNCS constraints0.000718845675244
ens_1d_8AAELECTRON MICROSCOPYNCS constraints0.000701687078965
ens_1d_9AAELECTRON MICROSCOPYNCS constraints0.000712209960517
ens_1d_10AAELECTRON MICROSCOPYNCS constraints0.000709836825773
ens_1d_11AAELECTRON MICROSCOPYNCS constraints0.000707400219001
ens_1d_12AAELECTRON MICROSCOPYNCS constraints0.000710413431192

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