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- PDB-5t3x: 3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylat... -

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Basic information

Entry
Database: PDB / ID: 5t3x
Title3.9 Angstrom Crystal Structure of a Fully and Natively Glycosylated BG505 SOSIP.664 HIV-1 Env Trimer in Complex with the Broadly Neutralizing Antibodies IOMA and 10-1074.
Components
  • (Envelope glycoprotein ...) x 2
  • 10-1074 Heavy Chain
  • 10-1074 Light Chain
  • IOMA Heavy Chain
  • IOMA Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / HIV / N-linked Glycosylation / Broadly Neutralizing Antibodies / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane ...positive regulation of plasma membrane raft polarization / positive regulation of receptor clustering / host cell endosome membrane / clathrin-dependent endocytosis of virus by host cell / viral protein processing / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / host cell plasma membrane / virion membrane / structural molecule activity / identical protein binding / membrane
Similarity search - Function
Envelope glycoprotein Gp160 / Retroviral envelope protein / Retroviral envelope protein GP41-like / Gp120 core superfamily / Envelope glycoprotein GP120 / Human immunodeficiency virus 1, envelope glycoprotein Gp120
Similarity search - Domain/homology
Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.9 Å
AuthorsGristick, H.B. / Bjorkman, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI100148 United States
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2016
Title: Natively glycosylated HIV-1 Env structure reveals new mode for antibody recognition of the CD4-binding site.
Authors: Gristick, H.B. / von Boehmer, L. / West, A.P. / Schamber, M. / Gazumyan, A. / Golijanin, J. / Seaman, M.S. / Fatkenheuer, G. / Klein, F. / Nussenzweig, M.C. / Bjorkman, P.J.
History
DepositionAug 26, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 19, 2016Group: Database references
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_struct_oper_list / 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_struct_oper_list.symmetry_operation / _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_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.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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 13, 2022Group: Author supporting evidence / Database references / Structure summary
Category: chem_comp / database_2 / pdbx_audit_support
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization / _pdbx_audit_support.grant_number
Revision 2.2Aug 16, 2023Group: Data collection / Other
Category: chem_comp_atom / chem_comp_bond / pdbx_database_status
Item: _pdbx_database_status.pdb_format_compatible
Revision 2.3Oct 4, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Revision 2.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,01725
Polymers167,8226
Non-polymers21,19519
Water00
1
B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules

B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules

B: Envelope glycoprotein gp160
G: Envelope glycoprotein gp160
H: 10-1074 Heavy Chain
L: 10-1074 Light Chain
D: IOMA Heavy Chain
E: IOMA Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)567,05175
Polymers503,46518
Non-polymers63,58657
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Unit cell
Length a, b, c (Å)217.509, 217.509, 156.009
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

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Envelope glycoprotein ... , 2 types, 2 molecules BG

#1: Protein Envelope glycoprotein gp160


Mass: 17146.482 Da / Num. of mol.: 1 / Fragment: UNP residues 509-611
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6
#2: Protein Envelope glycoprotein gp160


Mass: 54064.277 Da / Num. of mol.: 1 / Fragment: UNP residues 30-508
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: env / Production host: Homo sapiens (human) / References: UniProt: Q2N0S6

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Protein , 1 types, 1 molecules H

#3: Protein 10-1074 Heavy Chain


Mass: 25661.688 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Antibody , 3 types, 3 molecules LDE

#4: Antibody 10-1074 Light Chain


Mass: 23180.760 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#5: Antibody IOMA Heavy Chain


Mass: 25176.416 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#6: Antibody IOMA Light Chain


Mass: 22591.975 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

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Sugars , 17 types, 19 molecules

#7: Polysaccharide alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 367.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-6DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#8: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1a_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#9: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#10: 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
#11: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)]alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 2356.157 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-4[DGlcpNAcb1-2]DManpa1-3[DGalpb1-4DGlcpNAcb1-2[DGalpb1-4DGlcpNAcb1-4]DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,13,12/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-1-4-3-1-4-1-4-5/a4-b1_a6-m1_b4-c1_c3-d1_c6-h1_d2-e1_d4-f1_f4-g1_h2-i1_h4-k1_i4-j1_k4-l1WURCSPDB2Glycan 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)][b-D-GlcpNAc]{}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#12: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1787.631 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGalpb1-4DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-1-2-3-1-4-3-1-4-5/a4-b1_a6-j1_b4-c1_c3-d1_c6-g1_d2-e1_e4-f1_g2-h1_h4-i1WURCSPDB2Glycan 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)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#13: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1770.604 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/5,9,8/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-1-2-3-1-4-5-3-1/a4-b1_b4-c1_c3-d1_c6-h1_d2-e1_e4-f1_f6-g2_h2-i1WURCSPDB2Glycan 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)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#14: 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.: 3
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
#15: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)-alpha-D- ...alpha-D-mannopyranose-(1-2)-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: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-6DManpa1-6]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_f6-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]{[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#16: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-[beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]alpha-D-mannopyranose-(1-6)][2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 3141.860 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2[DGlcpNAcb1-4]DManpa1-3[DNeup5Aca2-6DGalpb1-4DGlcpNAcb1-2[DGalpb1-4DGlcpNAcb1-4]DManpa1-6][DGlcpNAcb1-4]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/6,16,15/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O][a1221m-1a_1-5]/1-1-2-3-1-4-5-1-1-3-1-4-5-1-4-6/a4-b1_a6-p1_b4-c1_c3-d1_c4-i1_c6-j1_d2-e1_d4-h1_e4-f1_f6-g2_j2-k1_j4-n1_k4-l1_l6-m2_n4-o1WURCSPDB2Glycan 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)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{}}[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(6+2)][a-D-Neup5Ac]{}}}[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#17: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-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: 1317.209 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-2DManpa1-3[DGlcpNAcb1-2DManpa1-6]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]/1-1-2-3-1-3-1/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f2-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)][b-D-GlcpNAc]{}}[(6+1)][a-D-Manp]{[(2+1)][b-D-GlcpNAc]{}}}}}}LINUCSPDB-CARE
#18: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,10,9/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-i1_i2-j1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#19: 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-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
#20: 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
#21: 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)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1056.964 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/4,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-3-3-4/a4-b1_a6-f1_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]{}}}[(6+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#22: 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
DManpa1-3DManpa1-6DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-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_c6-d1_d3-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#23: 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.: 1
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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Details

Has protein modificationY

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Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 4.23 Å3/Da / Density % sol: 70.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 200 mM ammonium citrate tribasic pH 7.0 100 mM imidazole pH 7.0 20% PEG MME 2,000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 12, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twinOperator: k,h,-l / Fraction: 0.16
ReflectionResolution: 3.9→80.63 Å / Num. obs: 25079 / % possible obs: 100 % / Redundancy: 18.2 % / CC1/2: 0.99 / Rmerge(I) obs: 0.35 / Rpim(I) all: 0.08 / Net I/σ(I): 7.6
Reflection shellResolution: 3.9→4.17 Å / Redundancy: 18.3 % / Rmerge(I) obs: 2.85 / Mean I/σ(I) obs: 1.5 / CC1/2: 0.3 / Rpim(I) all: 0.68 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
Cootmodel building
Aimlessdata scaling
iMOSFLMdata reduction
PHASER1.10.1-2155phasing
RefinementStarting model: 4TVP, 4FQ2, 4TNN, 4XVS

4tvp

4fq2

4tnn

4xvs


Resolution: 3.9→80.63 Å / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 44.46 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.3311 1276 5.09 %
Rwork0.296 --
obs0.3004 25058 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.9→80.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11194 0 1427 0 12621
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00313016
X-RAY DIFFRACTIONf_angle_d1.10817908
X-RAY DIFFRACTIONf_dihedral_angle_d13.8627559
X-RAY DIFFRACTIONf_chiral_restr0.0511956
X-RAY DIFFRACTIONf_plane_restr0.0052071
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.9007-4.05680.38181490.36232615X-RAY DIFFRACTION94
4.0568-4.24130.38391420.34192654X-RAY DIFFRACTION95
4.2413-4.46470.37061590.32552593X-RAY DIFFRACTION94
4.4647-4.74410.30131370.31842657X-RAY DIFFRACTION95
4.7441-5.10980.30571270.30782650X-RAY DIFFRACTION95
5.1098-5.62310.3131380.29762664X-RAY DIFFRACTION95
5.6231-6.43450.36341490.32522629X-RAY DIFFRACTION95
6.4345-8.09820.33361390.30912653X-RAY DIFFRACTION95
8.0982-43.41030.31151350.24392645X-RAY DIFFRACTION95
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)
10.1151-0.1957-0.15240.15340.09750.02441.6387-0.2813-0.85311.0101-0.0481-0.56530.3614-0.43340.00132.9422-1.0281-0.08042.68590.15941.9188-15.1248-11.4239126.6706
21.6607-2.13620.91423.9026-1.31981.0297-1.3794-0.5029-0.94072.53310.98280.1256-1.4641-0.41010.05651.1555-1.00670.35812.54370.85081.6272-9.22771.2999126.7059
30.0722-0.1273-0.00290.1111-0.03110.01410.4630.1410.2891-0.0033-0.73930.1157-0.0721-1.1742-03.05460.22740.2322.4073-0.06211.4154-24.3955.3223135.9566
40.0015-0.0099-0.00170.0246-0.00020.02070.058-0.72610.0209-0.34690.01620.22450.0130.2066-05.35830.70780.06922.4663-0.04521.55260.033714.7132145.6516
50.6054-0.24670.6063-0.19130.03840.44480.5865-0.148-0.76890.519-0.05890.5123-0.36510.42670.00012.10380.06680.15562.39390.29922.29-17.103-11.6983113.6082
60.8885-0.5176-0.71920.4827-0.12020.58630.39760.0333-0.09270.0211-0.2394-0.6768-0.13860.0769-0.00030.6966-0.1069-0.02720.94490.02991.0657-14.4988-11.751271.66
70.0939-1.0154-0.07030.41150.7231.33160.3992-0.3156-0.65290.0131-0.08410.2751-0.1755-0.21770.18080.7338-0.22710.10460.81260.29790.3792-28.1857-15.899993.5666
80.0828-0.0918-0.04360.12320.09560.0668-0.19350.3795-0.5599-0.37740.02560.2924-0.58320.5171-03.7571-0.5137-0.67251.99620.05582.904-41.669-46.746132.948
90.1506-0.10370.20580.2695-0.01240.2602-1.1636-0.5039-0.8228-1.0062-0.60380.0883-0.7741-0.6520.00012.518-0.379-0.50211.8895-0.20573.8035-38.8843-41.754845.5746
100.0898-0.05760.10660.057-0.07280.07210.4394-0.1896-0.0361-1.0120.8720.05860.3792-0.3702-0.00012.9107-0.0481-0.48832.93340.02763.4174-40.9838-39.912735.9926
110.8924-0.76990.2410.3677-0.0257-0.00050.5937-0.5431-0.3676-0.45360.50430.5970.11140.27570.2392.2549-0.6698-0.68450.7561-0.07891.9455-34.6996-45.960145.2163
120.1237-0.06070.00810.0838-0.04560.1116-0.39551.3431-0.881-0.2174-1.31570.5729-0.1683-1.1422-0.04184.6772-0.03180.06242.0124-0.90112.3836-31.4631-65.523721.443
130.0566-0.03890.07260.0114-0.03720.1099-0.89190.218-0.52820.076-0.7309-0.2849-0.9291-0.1218-0.00023.9043-0.9868-0.81392.6823-0.43363.2336-40.0014-70.820418.8579
140.0297-0.0656-0.02370.05170.03680.0065-0.5229-0.1578-0.5553-0.1991-0.8425-0.6098-0.03580.184502.57830.0438-0.5493.0267-0.91932.9645-11.9163-56.706451.3184
150.8454-0.37120.08510.71630.40050.36120.1254-0.3860.0017-1.55351.2094-0.52491.10820.13870.56511.8836-0.5157-0.74220.6834-0.87082.1871-23.4791-47.719452.0046
160.03430.0538-0.03120.0112-0.00750.0048-0.0890.1779-0.59430.34710.2148-0.9821-0.43260.3825-0.00021.6903-0.242-0.33371.873-0.31862.7695-22.346-54.461258.6412
170.13170.0077-0.10650.3335-0.50460.87550.7128-0.9006-0.1890.2591.09950.03410.1384-0.29510.4631.316-0.3417-0.36071.1507-0.72342.3862-24.4812-41.198952.2333
180.1837-0.16580.03110.1019-0.08790.09-0.09720.42650.2494-0.6235-0.5646-1.3748-0.2823-0.7221-0.00023.96880.8013-0.21172.978-0.59743.0282-21.7288-67.850623.9647
190.05090.0122-0.03440.0241-0.00390.0213-0.06340.1121-0.0684-0.13340.0850.2013-0.0352-0.13603.8296-1.09030.81764.5596-0.8125.2031-16.3847-68.332622.0349
20-0.0004-0.00680.0194-0.0082-0.00670.01640.16210.8494-0.8566-0.4153-0.19030.5807-0.18960.43920.00014.4688-0.50840.71383.1022-0.55793.9708-16.4295-64.844922.0823
21-0.0304-0.02210.01690.064-0.01830.01620.17220.95890.1945-0.0132-0.0269-0.03730.09410.016-0.00015.4368-2.0430.13614.7236-0.66342.3383-21.085-66.222411.5453
220.0136-0.02470.02710.0167-0.01080.02730.50350.2380.6448-0.2366-0.34810.05020.0720.24860.00013.9886-0.60960.66244.794-0.14933.5306-13.433-72.951413.7661
230.01130.03410.00950.0407-0.04950.0332-0.09290.32320.2157-0.10560.7889-0.01670.3547-0.2952-0.00014.5972-0.2437-0.37354.7954-0.17762.4105-16.0113-77.341916.1783
240.0748-0.33140.17180.4641-0.2684-0.0398-0.1091-0.09550.3751-0.0745-0.29580.33750.3113-0.172900.96440.03130.09141.509-0.06531.404-42.7557.988577.9873
250.0683-0.1330.08590.0677-0.10490.0346-0.17340.05610.4314-0.4652-1.1957-0.20680.0275-0.6008-0.00022.9740.05730.04733.93110.40294.0331-65.626230.433960.4412
260.21870.10990.00440.05160.00590.01460.05350.026-0.04480.08340.0580.1295-0.1388-0.06560.00125.5284-1.06971.01786.826-0.54493.0133-80.380835.357253.8697
270.39630.08040.22760.56870.60050.3627-0.2849-0.09070.12610.36-0.36490.5738-0.5271-0.5606-0.0061.24650.29630.24111.9217-0.68432.0348-52.807720.376794.4008
280.2910.0852-0.23381.69861.27881.28061.06681.01760.9375-2.18321.16010.4786-0.1575-1.09530.3553.08410.3996-2.67943.66070.19636.6124-75.456922.299168.3839
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 518 through 571 )
2X-RAY DIFFRACTION2chain 'B' and (resid 572 through 610 )
3X-RAY DIFFRACTION3chain 'B' and (resid 611 through 650 )
4X-RAY DIFFRACTION4chain 'B' and (resid 651 through 664 )
5X-RAY DIFFRACTION5chain 'G' and (resid 33 through 98 )
6X-RAY DIFFRACTION6chain 'G' and (resid 99 through 190 )
7X-RAY DIFFRACTION7chain 'G' and (resid 191 through 505 )
8X-RAY DIFFRACTION8chain 'H' and (resid 1 through 23 )
9X-RAY DIFFRACTION9chain 'H' and (resid 24 through 63 )
10X-RAY DIFFRACTION10chain 'H' and (resid 64 through 90 )
11X-RAY DIFFRACTION11chain 'H' and (resid 91 through 124 )
12X-RAY DIFFRACTION12chain 'H' and (resid 125 through 184 )
13X-RAY DIFFRACTION13chain 'H' and (resid 185 through 216 )
14X-RAY DIFFRACTION14chain 'L' and (resid 8 through 22 )
15X-RAY DIFFRACTION15chain 'L' and (resid 23 through 44 )
16X-RAY DIFFRACTION16chain 'L' and (resid 45 through 84 )
17X-RAY DIFFRACTION17chain 'L' and (resid 85 through 101 )
18X-RAY DIFFRACTION18chain 'L' and (resid 102 through 130 )
19X-RAY DIFFRACTION19chain 'L' and (resid 131 through 151 )
20X-RAY DIFFRACTION20chain 'L' and (resid 152 through 172 )
21X-RAY DIFFRACTION21chain 'L' and (resid 173 through 188 )
22X-RAY DIFFRACTION22chain 'L' and (resid 189 through 198 )
23X-RAY DIFFRACTION23chain 'L' and (resid 199 through 212 )
24X-RAY DIFFRACTION24chain 'D' and (resid 1 through 125 )
25X-RAY DIFFRACTION25chain 'D' and (resid 126 through 211 )
26X-RAY DIFFRACTION26chain 'D' and (resid 212 through 216 )
27X-RAY DIFFRACTION27chain 'E' and (resid 2 through 114 )
28X-RAY DIFFRACTION28chain 'E' and (resid 115 through 210 )

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  • 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

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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

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