[English] 日本語
Yorodumi
- PDB-7ol4: Mouse contactin-1 neurofascin-155 immunoglobulin domains adhesion... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ol4
TitleMouse contactin-1 neurofascin-155 immunoglobulin domains adhesion complex
Components
  • Contactin-1
  • Neurofascin
KeywordsCELL ADHESION / Heterophilic complex / Immunoglobulin cell adhesion protein / Neural cell adhesion protein / Horseshoe
Function / homology
Function and homology information


: / : / central nervous system myelin formation / cell-cell adhesion mediator activity / positive regulation of sodium ion transport / Notch signaling pathway / myelination / cerebellum development / locomotory behavior / axon guidance ...: / : / central nervous system myelin formation / cell-cell adhesion mediator activity / positive regulation of sodium ion transport / Notch signaling pathway / myelination / cerebellum development / locomotory behavior / axon guidance / brain development / positive regulation of neuron projection development / cell-cell adhesion / neuron projection development / positive regulation of peptidyl-tyrosine phosphorylation / myelin sheath / gene expression / carbohydrate binding / membrane raft / axon / positive regulation of gene expression / plasma membrane
Similarity search - Function
Contactin-1 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. ...Contactin-1 / Immunoglobulin / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / Fibronectin type III domain / Fibronectin type 3 domain / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Fibronectin type-III domain profile. / Fibronectin type III / Fibronectin type III superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 4.8 Å
AuthorsChataigner, L.M.P. / Janssen, B.J.C.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: Nat Commun / Year: 2022
Title: Structural insights into the contactin 1 - neurofascin 155 adhesion complex.
Authors: Chataigner, L.M.P. / Gogou, C. / den Boer, M.A. / Frias, C.P. / Thies-Weesie, D.M.E. / Granneman, J.C.M. / Heck, A.J.R. / Meijer, D.H. / Janssen, B.J.C.
History
DepositionMay 19, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Contactin-1
B: Contactin-1
C: Neurofascin
D: Neurofascin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)287,60622
Polymers273,0774
Non-polymers14,52918
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21290 Å2
ΔGint206 kcal/mol
Surface area136910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.773, 151.775, 162.340
Angle α, β, γ (deg.)90.000, 111.780, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))
21(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))
12(chain C and (resid 24 through 623 or resid 624...
22(chain D and (resid 24 through 234 or resid 248...

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A37 - 604
121(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A605 - 607
131(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A609
141(chain A and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))A616 - 618
211(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B37 - 604
221(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B605 - 607
231(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B609
241(chain B and (resid 37 through 604 or resid 605 through 607 or resid 609 or resid 616 through 618))B616 - 618
112(chain C and (resid 24 through 623 or resid 624...C24 - 623
122(chain C and (resid 24 through 623 or resid 624...C624 - 630
132(chain C and (resid 24 through 623 or resid 624...C636
142(chain C and (resid 24 through 623 or resid 624...C639
152(chain C and (resid 24 through 623 or resid 624...C641
162(chain C and (resid 24 through 623 or resid 624...C644
172(chain C and (resid 24 through 623 or resid 624...C646
212(chain D and (resid 24 through 234 or resid 248...D24 - 234
222(chain D and (resid 24 through 234 or resid 248...D248 - 623
232(chain D and (resid 24 through 234 or resid 248...D624 - 630
242(chain D and (resid 24 through 234 or resid 248...D632
252(chain D and (resid 24 through 234 or resid 248...D635
262(chain D and (resid 24 through 234 or resid 248...D637
272(chain D and (resid 24 through 234 or resid 248...D640
282(chain D and (resid 24 through 234 or resid 248...D642

NCS ensembles :
ID
1
2

-
Components

-
Protein , 2 types, 4 molecules ABCD

#1: Protein Contactin-1 / Neural cell surface protein F3


Mass: 66907.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Cntn1 / Production host: Homo sapiens (human) / References: UniProt: P12960
#2: Protein Neurofascin


Mass: 69630.703 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. The promoter and 5' UTR for this variant have not ...Details: Transcript Variant: This variant (2) has multiple differences in the coding region but maintains the reading frame, compared to variant 1. The promoter and 5' UTR for this variant have not been determined. The resulting isoform (2) includes the third fibronectin type 3 (FNIII) repeat, lacks the mucin-like domain, and has several differences near the N-terminus, compared to isoform 1. Isoform 2 is also known as NF155, as described by Davis et al. (PMID: 8947556). https://www.ncbi.nlm.nih.gov/nuccore/NM_001160316.1
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nfasc / Production host: Homo sapiens (human)

-
Sugars , 12 types, 18 molecules

#3: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a3-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-[alpha-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-[alpha-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: 1072.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e6-f1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#8: Polysaccharide alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-6)-alpha-D-mannopyranose-(1-6)-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
DManpa1-6DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-6)-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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-3/a4-b1_b4-c1_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam 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]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#12: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1397.245 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-3[DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,8,7/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#13: Polysaccharide alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpb1-4DGlcpNAcb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a3-b1_b4-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#14: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6 / Feature type: SUBJECT OF INVESTIGATION
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

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 6.15 Å3/Da / Density % sol: 80 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 2% v/v TacsimateTM pH 5.0, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, and 16% w/v PEG 3,350

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 13, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 4.795→76 Å / Num. obs: 15712 / % possible obs: 88.5 % / Redundancy: 7.1 % / Biso Wilson estimate: 109.76 Å2 / CC1/2: 0.993 / Net I/σ(I): 4.5
Reflection shellResolution: 4.795→5.352 Å / Mean I/σ(I) obs: 1.3 / Num. unique obs: 786 / CC1/2: 0.399

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassification
PHENIX1.19.2refinement
XDSdata reduction
PHASERphasing
PDB_EXTRACT3.27data extraction
STARANISOdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7OK5

7ok5


Resolution: 4.8→75.38 Å / SU ML: 0.73 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 47.37 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3258 791 5.05 %RANDOM
Rwork0.2884 14872 --
obs0.2901 15663 48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 563.43 Å2 / Biso mean: 259.2276 Å2 / Biso min: 127.28 Å2
Refinement stepCycle: final / Resolution: 4.8→75.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18329 0 971 0 19300
Biso mean--301.68 --
Num. residues----2315
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A5595X-RAY DIFFRACTION6.018TORSIONAL
12B5595X-RAY DIFFRACTION6.018TORSIONAL
21C6032X-RAY DIFFRACTION6.018TORSIONAL
22D6032X-RAY DIFFRACTION6.018TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
4.8-5.090.210290.35232602695
5.1-5.490.3101350.326182586016
5.49-6.040.3713760.3431423149928
6.04-6.910.341390.33142594273350
6.91-8.710.33662520.30724553480588
8.71-75.380.31672800.26465217549799
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)
110.0186-0.01524.90426.1588-7.53956.3114-0.69410.5863-0.89032.02230.48890.8184-1.93720.3721-02.5456-0.1005-0.06271.9815-0.42511.367131.7686-34.412860.8355
211.81790.3851-5.79318.83261.55348.2164-1.06311.01440.0547-0.94990.35570.86530.88010.0461-0.00062.90160.03490.09021.70690.11851.111841.19375.263446.4171
311.40453.5750.72934.5025-0.20373.33610.5759-0.4861.16060.0781-0.9236-1.47730.87822.296-0.00932.966-0.0661-0.78072.3179-0.28741.194356.01761.98965.162
41.2422-6.1358-0.10554.5678-1.84995.3339-1.9593-0.13960.4526-0.18071.37860.07580.50990.36690.00273.12690.181-0.15131.826-0.21351.986145.441-36.955880.8915
55.36771.09474.64812.7802-5.5045.8423-0.27050.8094-1.0031-0.2258-0.2165-1.05090.87831.68730.00033.4361-0.04920.45232.5982-0.05752.919465.5149-70.021588.9197
6-0.5390.94760.1419-1.2355-0.3142-2.071-0.5481-2.3213-0.5398-5.0263-1.3457-2.7009-3.3745-2.9862-0.01994.0149-1.0521-0.02397.13761.43145.920498.9861-62.647772.9801
77.34532.97782.3859.6155-1.12226.1051-0.1340.21230.4358-1.24740.0455-0.44911.0342-0.97180.00012.06060.30440.39771.6474-0.09012.05954.3878-37.81633.2159
85.9885-0.60142.96912.656210.95628.2002-0.0102-0.8006-0.1608-2.41230.31541.0529-1.5714-0.60730.00651.48690.18620.22011.8740.03651.572152.956-76.767420.6404
98.12121.73091.3274.7947-3.23873.4833-0.6634-1.48360.3726-0.8395-0.6736-1.7549-0.45190.2186-0.00191.36350.31060.39671.9912-0.12242.838776.3343-71.9617.1743
103.8796-1.21481.26597.5388-0.21862.1983-0.2722-0.0740.74661.66050.2594-0.67130.18090.37260.00012.58920.14630.72551.7903-0.07042.921678.1763-34.0269-2.7059
117.65374.81325.20215.6285-5.28183.19650.7064-1.49940.57171.1237-0.864-0.62241.08990.4610.00534.2185-0.01980.1192.34860.04582.28797.6252-1.65224.5034
12-1.1509-1.67890.2686-1.3905-0.2402-0.09620.4957-0.4652-7.64097.2308-4.32856.80380.08511.4957-1.09782.80450.5621-3.57177.07572.99163.4873112.1694-8.250939.3246
135.20312.2989-5.25075.70594.02023.3024-0.44051.3634-0.74638.2361-0.14194.5534.8463-7.5947-1.9675-19.12064.2463-6.63185.97272.52241.538.6586-1.658428.3213
148.73041.6501-1.906211.85525.10667.73390.0742-0.22450.41120.7016-0.51930.60640.52170.50440.00022.06370.0258-0.32551.5310.22571.412149.2951-16.829534.004
1510.953310.106-3.40167.3045-2.13677.48360.37862.32672.17960.22090.44191.1596-2.2754-1.13050.01232.55860.30540.69792.6444-0.30751.597847.752-11.032310.9999
165.62245.3301-0.67342.37470.68085.1958-1.14044.4275-1.56191.60831.78281.7757-1.49850.9701-0.0161-0.06080.13120.57236.3985-0.50794.93567.7293-5.83415.9907
170.2863-0.79712.22661.0014-1.43635.3797-2.38323.3976-1.40365.03145.1566-1.0497-7.4823-4.08081.1063.41732.0580.83937.31491.84614.591316.008429.03340.9727
180.07061.1001-1.26773.25870.29530.70272.4881-1.6641-0.27590.22710.30792.1987-3.4576-0.51061.18698.3198-0.96782.71473.75330.2034.747547.722140.236719.7372
192.898-5.50480.64755.24140.936410.5805-0.4579-0.6371-0.0995-1.3838-0.3411-0.30231.4952-2.3353-0.34211.2048-0.2384-0.49223.592-0.27152.594918.6833-74.576812.5206
205.0356-0.6195-7.474912.0736-2.45369.1241-0.51830.00130.344-1.68730.61940.1948-1.63711.90910.0032.1373-0.3280.13771.6479-0.09461.799550.5619-54.393635.5743
216.491-0.18123.86179.55470.41539.9331-0.935-0.5465-0.99350.37220.45120.96943.4018-0.6994-0.01363.2324-0.19350.49321.8432-0.17181.317833.5005-61.344850.934
223.21372.14132.0946-0.54180.822610.61620.0661-0.01510.8724-0.9796-0.5519-0.2780.5124-0.96230.00011.9259-0.03770.2023.4025-0.04953.73532.3496-74.730527.5264
234.1605-4.5721-4.24055.0212-3.23437.5108-1.5433-0.7399-0.88440.51110.392-0.2330.08890.27220.00033.5757-0.5139-0.12372.9373-0.09682.993514.3445-105.251739.5627
243.3248-1.78620.03071.5311-4.60355.07051.6762-0.0955-0.1870.7677-1.7858-1.74640.27270.85250.00014.4697-0.5717-0.15173.350.9173.110152.0643-105.781748.6126
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 133 )A35 - 133
2X-RAY DIFFRACTION2chain 'A' and ((resid 134 through 235 ) or (resid 605 through 607 ))A0
3X-RAY DIFFRACTION3chain 'A' and ((resid 236 through 328 ) or (resid 608 through 610 ))A0
4X-RAY DIFFRACTION4chain 'A' and ((resid 329 through 410 ) or (resid 611 through 611 ))A0
5X-RAY DIFFRACTION5chain 'A' and ((resid 411 through 503 ) or (resid 612 through 618 ))A0
6X-RAY DIFFRACTION6chain 'A' and (resid 504 through 604 )A504 - 604
7X-RAY DIFFRACTION7chain 'B' and (resid 37 through 133 )B37 - 133
8X-RAY DIFFRACTION8chain 'B' and ((resid 134 through 235 ) or (resid 605 through 608 ))B0
9X-RAY DIFFRACTION9chain 'B' and ((resid 236 through 328 ) or (resid 609 through 614 ))B0
10X-RAY DIFFRACTION10chain 'B' and ((resid 329 through 410 ) or (resid 615 through 615 ))B0
11X-RAY DIFFRACTION11chain 'B' and ((resid 411 through 503 ) or (resid 616 through 626 ))B0
12X-RAY DIFFRACTION12chain 'B' and (resid 504 through 604 )B504 - 604
13X-RAY DIFFRACTION13chain 'C' and (resid 24 through 131 )C24 - 131
14X-RAY DIFFRACTION14chain 'C' and (resid 132 through 234 )C132 - 234
15X-RAY DIFFRACTION15chain 'C' and ((resid 248 through 345 ) or (resid 635 through 639 ))C0
16X-RAY DIFFRACTION16chain 'C' and ((resid 346 through 438 ) or (resid 624 through 630 ))C0
17X-RAY DIFFRACTION17chain 'C' and ((resid 439 through 530 ) or (resid 640 through 648 ))C0
18X-RAY DIFFRACTION18chain 'C' and (resid 531 through 623 )C531 - 623
19X-RAY DIFFRACTION19chain 'D' and (resid 24 through 131 )D24 - 131
20X-RAY DIFFRACTION20chain 'D' and (resid 132 through 237 )D132 - 237
21X-RAY DIFFRACTION21chain 'D' and ((resid 248 through 345 ) or (resid 632 through 636 ))D0
22X-RAY DIFFRACTION22chain 'D' and ((resid 346 through 438 ) or (resid 624 through 631 ))D0
23X-RAY DIFFRACTION23chain 'D' and ((resid 439 through 530 ) or (resid 637 through 645 ))D0
24X-RAY DIFFRACTION24chain 'D' and (resid 531 through 623 )D531 - 623

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbjlvh1.pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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

Read more