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- PDB-4lxr: Structure of the Toll - Spatzle complex, a molecular hub in Droso... -

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Basic information

Entry
Database: PDB / ID: 4lxr
TitleStructure of the Toll - Spatzle complex, a molecular hub in Drosophila development and innate immunity
Components
  • Protein spaetzle C-106
  • Protein toll
KeywordsIMMUNE SYSTEM/CYTOKINE / TLR / LEUCINE-RICH REPEAT / IMMUNE SYSTEM / CYTOKINE RECEPTOR / EMBRYONIC DEVELOPMENT / INNATE IMMUNITY / RECEPTOR-LIGAND COMPLEX' / IMMUNE SYSTEM-CYTOKINE complex
Function / homology
Function and homology information


positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition ...positive regulation of antimicrobial peptide biosynthetic process / positive regulation of antifungal peptide biosynthetic process / positive regulation of hemocyte proliferation / regulation of embryonic pattern specification / Toll Like Receptor 10 (TLR10) Cascade / defense response to oomycetes / response to tumor cell / Formation of the trans-membrane 'signalling complex' / Adaptor protein complex binds to TL receptor at the plasma membrane / synaptic target inhibition / DL and DIF homodimers bind to TUB and phosphorylated PLL in the TL receptor 'signalling complex' / DL and DIF homodimers complexed with CACT are all phosphorylated in the TL receptor 'signalling complex' / Activated PLL kinase is autophosphorylated in the TL receptor 'signalling complex' / Phosphorylated CACT, DL and DIF homodimers dissociate from the TL receptor 'signalling complex' / PLL kinase binds to TUB in the TL receptor 'signalling complex' / positive regulation of antifungal peptide production / positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria / Toll binding / central nervous system formation / TIR domain binding / oocyte dorsal/ventral axis specification / cell competition in a multicellular organism / larval somatic muscle development / positive regulation of antimicrobial peptide production / antifungal innate immune response / Neutrophil degranulation / dorsal/ventral axis specification / Toll signaling pathway / detection of virus / NAD+ nucleotidase, cyclic ADP-ribose generating / dorsal/ventral pattern formation / motor neuron axon guidance / virion binding / cytokine receptor activity / negative regulation of multicellular organism growth / cytokine binding / cleavage furrow / defense response to fungus / synapse assembly / negative regulation of insulin receptor signaling pathway / cytokine activity / growth factor activity / response to hydrogen peroxide / negative regulation of cell growth / response to wounding / transmembrane signaling receptor activity / signaling receptor activity / heart development / defense response to Gram-negative bacterium / killing of cells of another organism / negative regulation of neuron apoptotic process / early endosome / receptor ligand activity / cell adhesion / defense response to Gram-positive bacterium / external side of plasma membrane / innate immune response / positive regulation of gene expression / cell surface / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane
Similarity search - Function
Spaetzle / Spaetzle / Leucine rich repeat C-terminal domain / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain ...Spaetzle / Spaetzle / Leucine rich repeat C-terminal domain / BspA type Leucine rich repeat region / BspA type Leucine rich repeat region (6 copies) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Cystine Knot Cytokines, subunit B / Cystine-knot cytokines / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Cystine-knot cytokine / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Ribbon / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Protein toll / Protein spaetzle
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.2 Å
AuthorsStelter, M. / Parthier, C. / Breithaupt, C. / Stubbs, M.T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Structure of the Toll-Spatzle complex, a molecular hub in Drosophila development and innate immunity.
Authors: Parthier, C. / Stelter, M. / Ursel, C. / Fandrich, U. / Lilie, H. / Breithaupt, C. / Stubbs, M.T.
History
DepositionJul 30, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 9, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein toll
J: Protein spaetzle C-106
K: Protein spaetzle C-106
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,55714
Polymers115,6463
Non-polymers3,91211
Water9,080504
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11500 Å2
ΔGint54 kcal/mol
Surface area41370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.025, 78.175, 124.450
Angle α, β, γ (deg.)90.00, 126.30, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 2 types, 3 molecules AJK

#1: Protein Protein toll


Mass: 89632.398 Da / Num. of mol.: 1 / Fragment: UNP residues 28-802
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Tl, CG5490 / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): Schneider 2 / References: UniProt: P08953
#2: Protein Protein spaetzle C-106


Mass: 13006.618 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: spz, CG6134 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta (DE3) / References: UniProt: P48607

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Sugars , 4 types, 10 molecules

#3: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#6: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 505 molecules

#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 504 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.92 Å3/Da / Density % sol: 57.82 %
Crystal growTemperature: 287 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 50 mM HEPES-Na salt, pH 7.5, vapor diffusion, hanging drop, temperature 287K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONBESSY 14.110.9184, 1.8448, 1.8454
2
Detector
TypeIDDetectorDate
MARMOSAIC 225 mm CCD1CCDSep 19, 2012
2
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1BESSY BL 14.1MADMx-ray1
2BESSY BL 14.1SINGLE WAVELENGTHMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
10.91841
21.84481
31.84541
ReflectionNumber: 43793 / Rmerge(I) obs: 0.15 / D res high: 3.91 Å / Num. obs: 22848 / % possible obs: 93.8
ReflectionResolution: 2.2→50 Å / Num. all: 68231 / Num. obs: 67514 / % possible obs: 98.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): -3 / Biso Wilson estimate: 52.183 Å2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 15.02
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.2-2.330.691.681,298.8
2.33-2.490.4342.731,299.5
2.49-2.690.2424.921,299.5
2.69-2.940.1328.521,299.3
2.94-3.290.07114.841,299.4
3.29-3.80.03626.51,299.1
3.8-4.640.02537.881,298.4
4.64-6.530.02241.961,297.8
6.53-500.01747.271,295.8

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
SOLOMONphasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.11data extraction
MAR345data collection
XDSdata reduction
XDSdata scaling
SHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.2→42.684 Å / Occupancy max: 1 / Occupancy min: 0.44 / SU ML: 0.25 / σ(F): 1.99 / Phase error: 23.33 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 3376 5 %
Rwork0.1757 --
obs0.1779 67506 99.27 %
all-67514 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 45.337 Å2
Refinement stepCycle: LAST / Resolution: 2.2→42.684 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7059 0 255 504 7818
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087527
X-RAY DIFFRACTIONf_angle_d1.13710201
X-RAY DIFFRACTIONf_dihedral_angle_d19.8992871
X-RAY DIFFRACTIONf_chiral_restr0.0731206
X-RAY DIFFRACTIONf_plane_restr0.0051299
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.22830.34751360.29472587X-RAY DIFFRACTION97
2.2283-2.26150.33181410.26222675X-RAY DIFFRACTION100
2.2615-2.29690.27671410.23872689X-RAY DIFFRACTION100
2.2969-2.33450.24781380.22972609X-RAY DIFFRACTION100
2.3345-2.37480.31420.22332706X-RAY DIFFRACTION100
2.3748-2.4180.25671390.22052646X-RAY DIFFRACTION100
2.418-2.46450.2791420.21122683X-RAY DIFFRACTION100
2.4645-2.51480.23711410.20152682X-RAY DIFFRACTION100
2.5148-2.56940.27831390.19212644X-RAY DIFFRACTION100
2.5694-2.62920.22141420.17892703X-RAY DIFFRACTION100
2.6292-2.69490.23311420.17582683X-RAY DIFFRACTION100
2.6949-2.76780.22071410.17772680X-RAY DIFFRACTION100
2.7678-2.84920.2521390.17912652X-RAY DIFFRACTION99
2.8492-2.94120.28691400.1942657X-RAY DIFFRACTION100
2.9412-3.04630.26271420.19312699X-RAY DIFFRACTION100
3.0463-3.16820.23531400.18822655X-RAY DIFFRACTION100
3.1682-3.31230.23421410.18752685X-RAY DIFFRACTION100
3.3123-3.48690.21591420.18992700X-RAY DIFFRACTION100
3.4869-3.70520.22391400.17632656X-RAY DIFFRACTION99
3.7052-3.99110.19841410.14942681X-RAY DIFFRACTION99
3.9911-4.39240.1671410.13512670X-RAY DIFFRACTION99
4.3924-5.02710.17121410.12572693X-RAY DIFFRACTION99
5.0271-6.33040.17581420.1672692X-RAY DIFFRACTION98
6.3304-42.69250.20161430.1832703X-RAY DIFFRACTION97
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.61751.1573-0.1253.4566-0.63762.7725-0.0316-0.78350.54151.00140.0704-0.249-0.63720.4144-0.110.49850.0977-0.04060.6334-0.21370.3328-73.7291-4.648631.0522
22.1936-0.78530.32380.6563-0.12330.66950.06920.24750.0521-0.1064-0.0586-0.10930.11970.0372-0.01020.1857-0.00650.01060.13270.01390.2044-52.4348-26.75464.2805
31.3498-0.01611.22250.0521-0.29542.0348-0.1584-0.41050.40420.79190.0359-0.0068-0.4723-0.27080.32220.74110.0831-0.21220.4025-0.18120.3969-13.6572-35.980937.7853
41.8881-0.0068-0.33183.24610.7952.491-0.03130.1155-0.3176-0.03520.3079-0.22410.59840.3249-0.24170.49640.1437-0.06530.3787-0.1360.33916.0886-46.510373.9068
52.4879-1.56370.76033.55542.49854.73430.1399-0.7517-0.91140.74230.1007-1.39930.79440.9614-0.08520.37970.1761-0.11030.68970.13310.5568-49.1306-29.008424.0238
60.1957-0.32120.02491.23570.23536.2381-0.3289-0.81870.37160.0901-0.25430.2886-0.4242-0.98380.50980.61770.289-0.28271.5776-0.21990.7908-44.6867-21.316734.7798
73.86992.27521.18833.89522.21298.1665-0.3052-0.68960.34921.12810.3426-0.6058-0.35840.96390.00640.53250.0933-0.18360.6301-0.04980.5001-46.7875-18.971626.9494
82.7232-1.60852.40686.5247-1.10364.9401-0.25240.05720.1646-0.23010.1807-0.08710.30850.1480.04950.113-0.02010.06970.19320.02270.2086-55.9151-23.14339.2751
93.64910.6044-0.26697.20542.92897.7134-0.0877-0.62040.63430.8032-0.054-0.1732-0.5830.1779-0.03450.3242-0.0193-0.09830.3736-0.12620.3725-52.7931-13.749625.8845
105.37692.27565.16573.02971.99364.9820.0533-0.89510.07160.64550.0422-0.4477-0.23670.1531-0.06270.31650.0274-0.07790.5041-0.04550.2979-53.5809-17.185824.886
115.1254-0.797-5.06152.85152.15325.68320.0816-0.64530.6316-0.17310.2183-0.94770.10391.6142-0.2270.74930.0406-0.14310.61510.10280.8016-57.9081-11.3595.1615
126.367-2.09330.07384.5105-0.4057.1384-0.1502-0.69130.8210.02450.1110.1077-0.9265-0.00470.04090.2778-0.004-0.05310.42620.00110.4745-61.8694-15.714317.5966
133.4241.01892.39775.82123.35528.15050.0216-0.62990.6360.8237-0.41020.2289-0.6525-0.32450.33180.49750.1173-0.03260.8162-0.14460.2311-63.8784-15.72235.5976
141.63660.06620.23464.46410.05943.8094-0.107-0.7734-0.57910.53730.03740.46950.2237-0.65290.25920.20460.01290.04940.38260.14430.3491-60.4703-31.906618.8642
153.40092.5725.046.09032.07098.1976-0.2505-0.330.02460.91280.0354-0.73130.13280.578-0.31080.4470.2398-0.040.97840.14770.317-57.5767-26.475534.157
165.815-3.3559-5.62247.61846.26287.0493-0.158-0.91620.12040.79760.5332-0.30230.39740.3018-0.24690.32010.1360.00780.72190.10720.2199-54.6622-27.968927.3681
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 28 through 100 )
2X-RAY DIFFRACTION2chain 'A' and (resid 101 through 479 )
3X-RAY DIFFRACTION3chain 'A' and (resid 480 through 649 )
4X-RAY DIFFRACTION4chain 'A' and (resid 650 through 800 )
5X-RAY DIFFRACTION5chain 'J' and (resid 5 through 11 )
6X-RAY DIFFRACTION6chain 'J' and (resid 12 through 16 )
7X-RAY DIFFRACTION7chain 'J' and (resid 17 through 56 )
8X-RAY DIFFRACTION8chain 'J' and (resid 57 through 64 )
9X-RAY DIFFRACTION9chain 'J' and (resid 65 through 94 )
10X-RAY DIFFRACTION10chain 'J' and (resid 95 through 104 )
11X-RAY DIFFRACTION11chain 'J' and (resid 105 through 110 )
12X-RAY DIFFRACTION12chain 'K' and (resid 1 through 11 )
13X-RAY DIFFRACTION13chain 'K' and (resid 12 through 47 )
14X-RAY DIFFRACTION14chain 'K' and (resid 48 through 66 )
15X-RAY DIFFRACTION15chain 'K' and (resid 67 through 94 )
16X-RAY DIFFRACTION16chain 'K' and (resid 95 through 107 )

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Jul 12, 2017. Major update of PDB

Major update of PDB

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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