[English] 日本語
Yorodumi
- PDB-6tyb: Isolation and Structure of an Antibody that Fully Neutralizes Iso... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tyb
TitleIsolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields
Components
  • (NEUTRALIZING ANTIBODY ITS90.03 FAB ...) x 2
  • Envelope glycoprotein gp160
  • T-cell surface glycoprotein CD4
KeywordsIMMUNE SYSTEM / bNABs / gp120 / fab / glycan
Function / homology
Function and homology information


induction by virus of host cell-cell fusion / cytokine production / membrane fusion involved in viral entry into host cell / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus ...induction by virus of host cell-cell fusion / cytokine production / membrane fusion involved in viral entry into host cell / helper T cell enhancement of adaptive immune response / interleukin-16 binding / interleukin-16 receptor activity / maintenance of protein location in cell / T cell selection / MHC class II protein binding / cellular response to granulocyte macrophage colony-stimulating factor stimulus / interleukin-15-mediated signaling pathway / positive regulation of monocyte differentiation / plasma membrane => GO:0005886 / regulation of calcium ion transport / macrophage differentiation / T cell differentiation / positive regulation of protein kinase activity / coreceptor activity / T cell activation / positive regulation of calcium-mediated signaling / protein tyrosine kinase binding / host cell endosome membrane / positive regulation of peptidyl-tyrosine phosphorylation / positive regulation of T cell activation / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / adaptive immune response / membrane => GO:0016020 / positive regulation of ERK1 and ERK2 cascade / positive regulation of viral entry into host cell / cell adhesion / symbiont entry into host cell / membrane raft / endoplasmic reticulum lumen / external side of plasma membrane / viral envelope / endoplasmic reticulum membrane / virion attachment to host cell / apoptotic process / host cell plasma membrane / structural molecule activity / positive regulation of DNA-templated transcription / virion membrane / signal transduction / protein homodimerization activity / zinc ion binding / plasma membrane
Similarity search - Function
CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Immunoglobulin ...CD4, extracellular / T cell CD4 receptor C-terminal region / CD4, extracellular / T cell CD4 receptor C terminal region / T-cell surface antigen CD4 / Immunoglobulin C2-set / Immunoglobulin C2-set domain / HIV Envelope Protein Gp120; Chain G / Human immunodeficiency virus 1, Gp160, envelope glycoprotein / Immunoglobulin / Immunoglobulin domain / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120 / Beta Complex / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Envelope glycoprotein gp160 / T-cell surface antigen T4/Leu-3 / T-cell surface glycoprotein CD4
Similarity search - Component
Biological speciesSimian immunodeficiency virus
Macaca mulatta (Rhesus monkey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.301 Å
AuthorsGorman, J. / Kwong, P.D.
CitationJournal: Immunity / Year: 2019
Title: Isolation and Structure of an Antibody that Fully Neutralizes Isolate SIVmac239 Reveals Functional Similarity of SIV and HIV Glycan Shields.
Authors: Gorman, J. / Mason, R.D. / Nettey, L. / Cavett, N. / Chuang, G.Y. / Peng, D. / Tsybovsky, Y. / Verardi, R. / Nguyen, R. / Ambrozak, D. / Biris, K. / LaBranche, C.C. / Ramesh, A. / Schramm, C. ...Authors: Gorman, J. / Mason, R.D. / Nettey, L. / Cavett, N. / Chuang, G.Y. / Peng, D. / Tsybovsky, Y. / Verardi, R. / Nguyen, R. / Ambrozak, D. / Biris, K. / LaBranche, C.C. / Ramesh, A. / Schramm, C.A. / Zhou, J. / Bailer, R.T. / Kepler, T.B. / Montefiori, D.C. / Shapiro, L. / Douek, D.C. / Mascola, J.R. / Roederer, M. / Kwong, P.D.
History
DepositionAug 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 30, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.page_first
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / struct_asym / struct_conn / 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 / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
G: Envelope glycoprotein gp160
C: T-cell surface glycoprotein CD4
H: NEUTRALIZING ANTIBODY ITS90.03 FAB HEAVY CHAIN
L: NEUTRALIZING ANTIBODY ITS90.03 FAB LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)120,50915
Polymers111,0594
Non-polymers9,45111
Water7,152397
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20280 Å2
ΔGint165 kcal/mol
Surface area46410 Å2
Unit cell
Length a, b, c (Å)197.143, 197.143, 178.531
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522

-
Components

-
Protein , 2 types, 2 molecules GC

#1: Protein Envelope glycoprotein gp160


Mass: 41117.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Gene: env / Production host: Homo sapiens (human) / Strain (production host): GNTI- / References: UniProt: E7CWP5
#2: Protein T-cell surface glycoprotein CD4


Mass: 20582.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Gene: CD4 / Production host: Homo sapiens (human) / Strain (production host): GNTI- / References: UniProt: F6XGD3, UniProt: P16003*PLUS

-
Antibody , 2 types, 2 molecules HL

#3: Antibody NEUTRALIZING ANTIBODY ITS90.03 FAB HEAVY CHAIN


Mass: 25868.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)
#4: Antibody NEUTRALIZING ANTIBODY ITS90.03 FAB LIGHT CHAIN


Mass: 23490.102 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Macaca mulatta (Rhesus monkey) / Production host: Homo sapiens (human)

-
Sugars , 7 types, 11 molecules

#5: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-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
#6: 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.: 1 / Source method: isolated from a natural 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
#7: 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 natural 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
#8: 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)]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
DManpa1-2DManpa1-3[DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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-f1_d2-e1_f3-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{}}}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D- ...alpha-D-mannopyranose-(1-2)-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: 1072.964 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam 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-f1_d2-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-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]{}}}}}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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#11: 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 natural 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

-
Non-polymers , 1 types, 397 molecules

#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 397 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.51 Å3/Da / Density % sol: 72.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 6% PEG 8000, 17% isopropanol, 0.1M imidazole pH 6.5. Crystals were flash frozen in liquid nitrogen with 20 % (v/v) ethylene glycol as a cryoprotectant.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→40 Å / Num. obs: 84058 / % possible obs: 92.7 % / Redundancy: 8.8 % / Rmerge(I) obs: 0.105 / Rpim(I) all: 0.034 / Rrim(I) all: 0.111 / Χ2: 0.966 / Net I/σ(I): 10.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.3-2.341.50.70820280.4640.5730.9170.81945.3
2.34-2.381.90.82426670.4930.5751.0140.90259.9
2.38-2.432.30.81433010.4480.5280.9820.89573.7
2.43-2.482.90.88837440.4390.5191.0410.89784.1
2.48-2.533.80.87941280.5830.450.9980.88891.9
2.53-2.595.10.85843820.6590.3860.9480.8997.9
2.59-2.666.90.86444520.7590.3370.9320.91899.8
2.66-2.739.10.84744720.840.2910.8970.91100
2.73-2.8110.60.65845030.9230.210.6920.914100
2.81-2.911.20.52745130.9510.1640.5520.917100
2.9-311.30.38744780.9670.120.4060.941100
3-3.1211.30.28145080.9820.0870.2950.943100
3.12-3.2611.20.19445170.990.060.2030.951100
3.26-3.4411.20.13945330.9930.0430.1460.956100
3.44-3.6511.20.10145420.9960.0310.1060.963100
3.65-3.9311.20.0845520.9970.0250.0841.01100
3.93-4.3311.10.06845730.9970.0210.0711.072100
4.33-4.9511.10.0646120.9980.0190.0631.082100
4.95-6.2410.90.05646630.9980.0170.0591.01100
6.24-4010.20.05348900.9980.0170.0550.97899.4

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIXdev_3584refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CAY
Resolution: 2.301→35.867 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.53
RfactorNum. reflection% reflection
Rfree0.2097 6541 5 %
Rwork0.1781 --
obs0.1796 76207 75.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 154.65 Å2 / Biso mean: 51.3624 Å2 / Biso min: 8.98 Å2
Refinement stepCycle: final / Resolution: 2.301→35.867 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7482 0 632 397 8511
Biso mean--91.34 42.87 -
Num. residues----954
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.3011-2.32730.4369220.38464258
2.3273-2.35460.3753360.325267312
2.3546-2.38330.3335450.315486716
2.3833-2.41350.3721640.2984112721
2.4135-2.44530.3272750.2865141626
2.4453-2.47870.3235920.284174632
2.4787-2.51410.29011080.2695220340
2.5141-2.55170.28141450.2512261048
2.5517-2.59150.30141730.2551310257
2.5915-2.6340.27661950.2416365067
2.634-2.67940.24752140.2424414276
2.6794-2.72810.27422480.233463285
2.7281-2.78060.26662690.2288506493
2.7806-2.83730.27882820.2322532698
2.8373-2.8990.25772880.22195475100
2.899-2.96640.24022890.2165443100
2.9664-3.04050.23982860.20255425100
3.0405-3.12270.26052900.19535459100
3.1227-3.21450.21292910.18925442100
3.2145-3.31820.20512900.18325443100
3.3182-3.43670.20682890.18245455100
3.4367-3.57420.2262840.17465450100
3.5742-3.73670.18022740.16045474100
3.7367-3.93350.19282930.15065444100
3.9335-4.17960.15642810.1385448100
4.1796-4.50170.14782850.12645449100
4.5017-4.95370.15242850.11975447100
4.9537-5.66810.17592880.14555466100
5.6681-7.13190.20492830.17715461100
7.1319-35.8670.21322770.1843542099
Refinement TLS params.

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

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
18.91214.2578-2.11517.6404-0.39964.412-0.26720.1188-0.0236-0.65220.3287-0.54180.1505-0.0121-0.02530.36990.1381-0.09870.3260.01250.471818.826333.8924.7552
21.0258-0.09120.37841.2711-0.0281.7945-0.1171-0.0976-0.10040.15480.1936-0.1920.27420.176-0.06310.1530.0701-0.00370.1816-0.01690.225711.284240.1497-1.0106
32.0508-0.01050.22452.91340.19981.8339-0.05470.1868-0.1363-0.24740.03870.29660.0325-0.38680.02010.0789-0.0244-0.00440.217-0.00150.1583-5.120945.9039-15.0883
41.3682-0.44770.07771.6641-0.05912.3372-0.06290.0895-0.1742-0.05390.1198-0.0750.1180.0223-0.04240.07480.00410.02750.1169-0.0350.19186.043342.8214-12.5019
52.81211.3848-2.09595.2014-2.85443.4821-0.0451-0.12540.2436-0.25680.0206-0.3271-0.57210.4657-0.00130.3915-0.17280.04290.28090.00130.357715.268361.4061-23.7474
61.9646-0.1534-0.22461.6103-2.3073.4061-0.04590.53380.0696-1.26580.0256-0.34530.4120.20330.08171.5456-0.34750.20.53510.00550.580322.7678.1196-48.5157
71.3884-1.1447-1.1752.35581.92223.2788-0.1394-0.20570.05120.29380.0813-0.0264-0.06430.11330.05320.34970.1375-0.06170.2495-0.05980.2018-0.656472.006223.5706
83.1409-0.49630.67512.69950.18851.9648-0.1567-0.3123-0.17380.51380.09790.7237-0.0982-0.46480.06360.66960.25350.11730.5064-0.06440.4448-27.792592.290438.2178
91.0825-0.8306-0.15350.90910.48640.9251-0.04150.03730.2137-0.2946-0.28390.2934-0.6582-0.4963-0.18460.55720.3434-0.12190.4175-0.20.3513-14.316777.84577.107
102.4722-0.5012-0.07173.59211.77543.23230.12840.14580.17620.1386-0.1385-0.1043-0.3275-0.1117-0.07520.82970.39390.00910.5573-0.12950.4387-25.5586104.605328.1701
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'G' and (resid 44 through 79 )G44 - 79
2X-RAY DIFFRACTION2chain 'G' and (resid 80 through 270 )G80 - 270
3X-RAY DIFFRACTION3chain 'G' and (resid 271 through 414 )G271 - 414
4X-RAY DIFFRACTION4chain 'G' and (resid 415 through 492 )G415 - 492
5X-RAY DIFFRACTION5chain 'C' and (resid 1 through 97 )C1 - 97
6X-RAY DIFFRACTION6chain 'C' and (resid 98 through 176 )C98 - 176
7X-RAY DIFFRACTION7chain 'H' and (resid 1 through 113 )H1 - 113
8X-RAY DIFFRACTION8chain 'H' and (resid 114 through 214 )H114 - 214
9X-RAY DIFFRACTION9chain 'L' and (resid 1 through 113 )L1 - 113
10X-RAY DIFFRACTION10chain 'L' and (resid 114 through 213 )L114 - 213

+
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://pdbjlc1.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