[English] 日本語
Yorodumi
- PDB-5fyj: Crystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5fyj
TitleCrystal Structure at 3.4 A Resolution of Fully Glycosylated HIV-1 Clade G X1193.c1 SOSIP.664 Prefusion Env Trimer in Complex with Broadly Neutralizing Antibodies PGT122, 35O22 and VRC01
Components
  • (35O22) x 2
  • (PGT122) x 2
  • GP120 ENV ECTODOMAIN
  • GP41 ENV ECTODOMAIN
  • VRC01
KeywordsVIRAL PROTEIN / HIV / ENVELOPE / GLYCAN / TRIMER
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 ...: / 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 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRIC ACID / Envelope glycoprotein gp160
Similarity search - Component
Biological speciesHUMAN IMMUNODEFICIENCY VIRUS 1
HOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsStewart-Jones, G.B.E. / Zhou, T. / Thomas, P.V. / Kwong, P.D.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2016
Title: Trimeric HIV-1-Env Structures Define Glycan Shields from Clades A, B and G
Authors: Stewart-Jones, G.B.E. / Soto, C. / Lemmin, T. / Chuang, G.Y. / Druz, A. / Kong, R. / Thomas, P.V. / Wagh, K. / Zhou, T. / Behrens, A.J. / Bylund, T. / Choi, C.W. / Davison, J.R. / Georgiev, ...Authors: Stewart-Jones, G.B.E. / Soto, C. / Lemmin, T. / Chuang, G.Y. / Druz, A. / Kong, R. / Thomas, P.V. / Wagh, K. / Zhou, T. / Behrens, A.J. / Bylund, T. / Choi, C.W. / Davison, J.R. / Georgiev, I.S. / Joyce, M.G. / Kwon, Y.D. / Pancera, M. / Taft, J. / Yang, Y. / Zhang, B. / Shivatare, S.S. / Shivatare, V.S. / Lee, C.C.D. / Wu, C.Y. / Bewley, C.A. / Burton, D.R. / Koff, W.C. / Connors, M. / Crispin, M. / Korber, B.T. / Wong, C.H. / Mascola, J.R. / Kwong, P.D.
History
DepositionMar 8, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
Revision 1.2May 18, 2016Group: Database references
Revision 1.3Jul 27, 2016Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary
Revision 1.4Aug 3, 2016Group: Structure summary
Revision 1.5Jul 12, 2017Group: Advisory / Derived calculations / Category: database_PDB_caveat / struct_conn
Item: _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag ..._struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Other / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_database_status / 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_chiral / pdbx_validate_symm_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.pdbx_PDB_ins_code / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_PDB_ins_code / _struct_conn.pdbx_ptnr2_PDB_ins_code / _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 2.1Jan 10, 2024Group: 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
Revision 2.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)253,21640
Polymers223,6698
Non-polymers29,54732
Water21612
1
B: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
hetero molecules

B: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
hetero molecules

B: GP41 ENV ECTODOMAIN
D: 35O22
E: 35O22
G: GP120 ENV ECTODOMAIN
H: PGT122
L: PGT122
U: VRC01
V: VRC01
hetero molecules


Theoretical massNumber of molelcules
Total (without water)759,648120
Polymers671,00624
Non-polymers88,64296
Water32418
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
Buried area130110 Å2
ΔGint239.5 kcal/mol
Surface area248470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)127.160, 127.160, 313.650
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63

-
Components

-
Protein , 3 types, 3 molecules BGH

#1: Protein GP41 ENV ECTODOMAIN


Mass: 17990.371 Da / Num. of mol.: 1 / Fragment: GP41 ENV ECTODOMAIN, RESIDUES 510-663 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Cell: T-CELL / Gene: ENV / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: C6ZIG9
#4: Protein GP120 ENV ECTODOMAIN


Mass: 54536.035 Da / Num. of mol.: 1 / Fragment: GP120 ENV ECTODOMAIN, RESIDUES 32-506 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN IMMUNODEFICIENCY VIRUS 1 / Cell: T-CELL / Gene: ENV / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human) / References: UniProt: C6ZIG9
#5: Protein PGT122


Mass: 26465.877 Da / Num. of mol.: 1 / Fragment: PGT122 ANTIBODY FAB HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)

-
Antibody , 4 types, 5 molecules DELUV

#2: Antibody 35O22


Mass: 26170.533 Da / Num. of mol.: 1 / Fragment: 35O22 ANTIBODY FAB HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)
#3: Antibody 35O22


Mass: 23318.824 Da / Num. of mol.: 1 / Fragment: 35O22 ANTIBODY FAB LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)
#6: Antibody PGT122


Mass: 22880.275 Da / Num. of mol.: 1 / Fragment: PGT122 ANTIBODY FAB LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)
#7: Antibody VRC01


Mass: 26153.303 Da / Num. of mol.: 2 / Fragment: VRC01 ANTIBODY FV LIGHT CHAIN / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell: B-CELL / Plasmid: PVRC8400 / Cell line (production host): HEK-293T GNTI- / Production host: HOMO SAPIENS (human)

-
Sugars , 15 types, 27 molecules

#8: 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.: 4
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
#9: 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-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
#10: 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-Glycam 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
[]{[(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]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#11: 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-(1-3)-[alpha-D-mannopyranose-(1-2)-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: 1883.668 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,11,10/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_g6-j1_h2-i1_j2-k1WURCSPDB2Glycan 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]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#12: 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-(1-3)-[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: 1721.527 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3[DManpa1-6]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-j1_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)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#13: 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.: 1
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
#14: 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
#15: 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-(1-3)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-2DManpa1-3[DManpa1-2DManpa1-3DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[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/a4-b1_b4-c1_c3-d1_c6-g1_d2-e1_e2-f1_g3-h1_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)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#16: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-6[DManpa1-3]DManpa1-6[DManpa1-2DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[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/a4-b1_b4-c1_c3-d1_c6-f1_d2-e1_f3-g1_f6-h1_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)][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
#17: 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.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-6DManpa1-6[DManpa1-3]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-e1_e6-f1WURCSPDB2Glycan 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-D-Manp]{}}}}}}LINUCSPDB-CARE
#18: 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-(1-3)]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
DManpa1-2DManpa1-3DManpa1-6[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_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]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#19: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-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: 1559.386 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,9,8/[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/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-h1_f2-g1_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]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#20: Polysaccharide alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-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: 1721.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-2DManpa1-3[DManpa1-2DManpa1-6]DManpa1-6[DManpa1-2DManpa1-3]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-f1_d2-e1_f3-g1_f6-i1_g2-h1_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]{}}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}[(6+1)][a-D-Manp]{[(2+1)][a-D-Manp]{}}}}}}}LINUCSPDB-CARE
#21: 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-(1-6)]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
DManpa1-2DManpa1-2DManpa1-3[DManpa1-6]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-g1_d2-e1_e2-f1WURCSPDB2Glycan 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]{}}}}}LINUCSPDB-CARE
#24: 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.: 3
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

-
Non-polymers , 3 types, 17 molecules

#22: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#23: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#25: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 12 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.42 % / Description: NONE
Crystal growpH: 4.5
Details: 4.95% ISOPROPANOL, 8.25% PEG 3350, 0.2M AMMONIUM CITRATE PH 4.5

-
Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Feb 8, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 51684 / % possible obs: 99.7 % / Observed criterion σ(I): 2 / Redundancy: 6 % / Rmerge(I) obs: 0.14 / Net I/σ(I): 9.05

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4TVP

4tvp


Resolution: 3.11→44.654 Å / σ(F): 1.35 / Phase error: 30.67 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2733 2011 4.7 %
Rwork0.2144 --
obs0.2166 42755 83.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.11→44.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13482 0 1982 12 15476
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00515968
X-RAY DIFFRACTIONf_angle_d1.01421973
X-RAY DIFFRACTIONf_dihedral_angle_d14.8366310
X-RAY DIFFRACTIONf_chiral_restr0.0392916
X-RAY DIFFRACTIONf_plane_restr0.0042495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.1314-3.20970.2964180.2873410X-RAY DIFFRACTION11
3.2097-3.29640.3863470.2691006X-RAY DIFFRACTION28
3.2964-3.39330.3557940.26661949X-RAY DIFFRACTION55
3.3933-3.50270.33421550.25613140X-RAY DIFFRACTION87
3.5027-3.62770.26911660.25083371X-RAY DIFFRACTION94
3.6277-3.77280.28481680.23293397X-RAY DIFFRACTION95
3.7728-3.94420.27941650.22763413X-RAY DIFFRACTION95
3.9442-4.15180.26471620.21093420X-RAY DIFFRACTION95
4.1518-4.41140.25261730.19343445X-RAY DIFFRACTION95
4.4114-4.75110.26641690.18573412X-RAY DIFFRACTION95
4.7511-5.22760.24641700.1933413X-RAY DIFFRACTION95
5.2276-5.98020.30951730.21543423X-RAY DIFFRACTION95
5.9802-7.520.31481680.23243449X-RAY DIFFRACTION95
7.52-33.24720.23361750.1923455X-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)
11.60310.9898-0.94633.46942.00282.5633-0.1612-0.0250.06910.523-0.70321.0424-0.4534-0.4444-0.15460.41570.1096-0.0080.3641-0.15460.443944.298628.8359-24.512
20.10670.433-0.23611.1583-0.99960.6863-0.6165-0.01860.7648-0.2666-0.17410.0581-0.156-0.08290.47890.8461-0.10690.33871.2328-0.05260.975248.706642.8738-4.5755
31.4008-0.8556-2.98051.46092.87989.8134-1.1622-1.4348-0.17761.35931.42840.2790.4318-0.01150.2081-1.1659-2.0165-0.1805-2.5698-0.35430.535659.870830.6028-11.8037
42.23270.05-0.33543.8160.5540.1718-0.454-0.10720.0612-0.54010.0602-1.0951-0.59430.2524-0.2080.3422-0.0272-0.07490.3082-0.18130.279360.941522.8309-34.1947
54.6053-0.8934-0.45573.14330.53051.6244-0.9631-0.7475-0.9640.0673-0.9882-0.27751.32422.2991-0.12970.71790.08440.2227-0.6458-0.49440.340251.34311.6075-30.095
67.6253.2033-2.78344.379-0.73152.7221-1.94821.38070.9359-0.5774-0.0578-0.9333-1.18751.2895-0.2367-0.17150.85290.6774-0.1427-0.6723-0.258674.275923.3793-34.3531
72.97040.6954-0.52392.7496-0.01930.53320.62510.0556-0.9101-0.56690.41070.83220.37671.0233-0.1840.553-0.8566-0.23-1.4572-0.70361.239524.8395-1.7948-31.5552
81.42910.8053-0.54871.8954-0.03441.09570.04410.3653-0.22960.4695-0.11511.13270.1817-0.0554-0.18360.8211-0.1536-0.00650.5187-0.2821.104623.6371-0.3008-33.2572
90.47480.0442-0.34480.01640.02810.1563-0.72330.4987-0.9832-0.3729-0.3401-0.03780.82151.4594-0.41422.4311-0.2891-0.1150.2285-0.70411.617630.1144-31.9952-33.5182
101.8269-0.22430.45241.6135-1.15450.6749-0.082-0.4835-0.4747-0.2943-0.83840.1314-0.10630.6408-0.22961.0097-0.26060.20711.0307-0.04781.640830.9775-32.6802-29.2893
111.9552-0.3108-0.62783.18180.86941.19470.2560.2717-0.5974-1.5707-0.05960.06160.15950.3337-0.36071.2485-0.1732-0.15421.0781-0.43930.913337.1959-0.5139-51.6327
120.34-0.1808-0.02750.31460.08720.0104-0.1834-0.13940.14140.11080.11280.10140.24960.5532-0.03482.10080.1660.07831.308-0.52741.466231.0598-34.8616-41.6497
130.7971-0.31610.14164.7894-1.51210.40190.0159-0.0454-0.8162-0.41340.1838-0.07831.543-1.1594-0.13421.7779-0.0515-0.30910.8384-0.51892.571427.9852-32.4323-47.4202
143.6906-0.7173-1.86860.94930.9991.3620.94230.0203-0.3141-0.25370.47860.6080.13630.2012-0.0082.101-0.11310.25080.66190.01071.859427.3017-44.5651-45.8868
150.6890.16741.0934-0.1081-0.10772.4177-0.2036-0.40550.14210.3428-0.16190.0057-0.09-0.11190.03160.5127-0.03880.14060.4124-0.06620.666646.597927.3407-4.3694
162.069-0.2345-0.64632.5085-0.3962.73030.1081-1.0541-0.50290.84790.50920.3170.0733-0.30230.5131.04570.08320.00171.43960.07230.580940.242728.777242.5901
171.9754-0.0081-0.76492.68220.01820.3971-0.4116-0.6763-0.47780.3981-0.2384-0.0860.1793-0.56410.24280.9778-0.1160.06931.2066-0.11070.614547.515628.35840.7242
180.7323-0.4487-0.99770.8564-1.25250.90250.1214-0.4098-0.26110.226-0.24690.33590.1086-0.5673-0.00430.6933-0.14370.11420.6533-0.10290.53735.536821.32753.9494
191.6155-0.0960.9971.4774-0.94041.0762-1.48290.1861.03680.1039-0.14050.1183-0.5391-1.0309-0.15820.1362-0.60321.5761.5687-0.4681-0.476230.356321.362723.0895
204.41640.07961.58332.0242-0.99432.3011-0.0627-0.2705-0.4947-0.57830.15821.15691.4783-0.3087-0.0621.0013-0.1110.26561.6425-0.28330.792923.484817.834321.2876
211.18061.15341.00191.15380.58230.9872-0.4868-0.3160.08010.9599-0.1457-0.13750.13990.5754-0.00341.127-0.16860.09121.2662-0.10190.41236.591324.18922.0229
222.3469-0.3883-0.38362.58370.78632.3261-0.3197-0.1719-0.61290.5647-0.20610.04390.45220.0670.10750.3025-0.1901-0.0410.2252-0.20220.643944.758413.8109-8.6675
230.9498-0.064-0.02850.2976-0.53521.4168-0.3308-0.3855-0.10450.62660.4590.85830.1532-1.03910.21161.5906-0.70850.35212.3641-0.38390.7614-0.152924.503967.1841
244.5916-1.51042.02946.1512-0.75315.49330.2535-0.3793-0.3602-0.258-0.10850.09161.2242-0.38740.34691.75080.21180.70271.7947-0.65550.49998.54333.843765.2983
252.293-1.44872.29111.2298-1.9333.00670.5891.1031-0.5879-1.8818-0.14610.33341.00260.7328-0.3211.80150.53351.86462.0678-0.34120.16919.89721.557958.4677
260.2923-0.0865-0.57010.01210.26861.04890.02140.1502-1.15650.45691.01260.05410.8696-0.55770.2591.30750.07910.271.9253-0.49350.91449.863925.10457.6997
271.42850.4692-0.31722.396-0.73691.61030.2631.0519-0.0606-0.07880.2453-0.16090.6492-0.1282-0.19831.4735-0.07240.92972.001-1.26120.66290.221335.998179.6829
281.8927-0.19410.97551.93780.21720.5367-0.07150.2994-0.567-0.2714-0.09780.0528-0.04210.3739-0.31211.1871-0.1020.22642.1115-0.30680.7284-10.43445.192684.4645
291.03460.1371-0.3581.7618-1.42730.9523-0.09340.1589-0.05470.1298-0.13590.6415-1.0001-0.9287-0.03851.12430.14930.09971.9017-0.21160.80938.70244.124551.292
304.2799-4.6173-2.99939.55254.17712.31630.0953-0.58140.3720.5768-0.217-0.76840.0720.12330.15241.6521-0.2001-0.30042.4669-0.40330.57251.851259.241264.2938
311.95350.59620.11952.02030.58170.1097-0.03310.33710.0651-0.41560.02410.33270.554-0.19770.08161.7941-0.05430.05072.1588-0.02820.5687-0.705856.558286.1162
326.209-1.4669-0.78937.72771.76290.4606-0.6987-0.4323-0.21060.12940.56740.369-0.25010.10040.03911.40930.00340.021.2949-0.05350.6911-1.650861.475390.8723
335.34552.6608-1.08675.312-2.13730.8460.1454-1.3623-0.32270.8591-0.62980.538-0.50330.44160.54371.14460.4832-0.62551.16930.51020.997461.6042-0.41920.7813
341.99851.0523-4.93352.94450.57571.952-0.34980.0735-0.2562-0.03110.1091-0.2812-0.05080.16860.38341.74660.5648-0.07721.4734-0.05870.673548.557-8.857538.156
352.26020.0158-0.79674.44520.67820.5576-0.2213-0.6227-0.29470.6489-0.03470.28210.023-0.11480.36331.4217-0.07430.49030.62040.24281.307954.20484.345622.0157
361.31640.739-0.71746.37051.16080.79960.0578-0.1887-0.31250.06210.07580.26110.18910.04110.16092.53250.67270.10281.18540.18931.78245.6228-12.374621.3145
376.85-3.5816-0.41535.96014.03733.5978-0.23170.1149-0.12340.1294-0.04150.0403-0.04310.0372-0.0060.7106-0.6230.84770.10211.22081.095945.77197.267219.3142
381.5471.5944-0.9851.6226-1.02430.648-0.4008-0.5308-0.33471.03-0.26040.54190.14720.54060.22591.63720.01570.92771.05280.31870.918437.5352-2.398423.816
394.0050.50120.81286.22482.86781.40310.2574-0.20470.3860.0796-0.38970.25180.1936-0.07320.2241.72160.18050.43411.12660.29180.19349.48675.354228.5497
404.25080.13721.95460.62231.60914.82670.2592-0.0059-0.07970.2113-0.0896-0.3935-0.2620.2959-0.02081.5269-0.2350.90231.15980.26441.767545.1949-11.112931.1008
412.0162-1.210.48591.77430.11732.1181-0.35150.26940.39290.02860.0357-0.2508-0.8261-0.63390.20831.21540.36580.34771.76640.3831.823653.61661.469712.2973
421.83230.1661-0.97524.2712-1.75775.26-0.2678-0.4431-0.7878-0.1183-0.4886-0.67010.05830.87740.79191.64490.12830.2320.80930.26161.042953.2781-6.18119.0148
430.03650.12850.00720.3838-0.0278-0.0098-0.58780.1799-0.06640.09840.01320.298-0.22650.11020.36932.07360.43120.12211.5941-0.1082.487351.1863-24.68985.925
440.24360.4249-0.3290.735-0.31942.46680.44540.3124-0.5598-0.5456-0.1276-0.0042-0.12720.8054-0.77912.0180.5558-0.19381.4974-0.54141.927746.4063-12.67845.9674
454.679-2.84781.60691.7579-0.97910.54650.0156-0.5003-0.0802-0.1687-0.16120.2002-0.5159-0.0040.09561.2831-0.4491-0.20111.23360.27091.721359.3625-13.115214.3113
464.34081.49681.56841.2291-0.92363.5228-0.055-0.14430.2520.16930.2236-0.1589-0.38590.58370.0291.53150.14220.92231.13660.0561.288560.0782-11.11412.2682
471.34270.2252-0.67890.0433-0.12440.3373-0.23720.52-1.0187-0.02060.36510.25570.28770.2111-0.24371.42750.46960.40331.0489-0.37571.584749.1685-16.4207-2.4274
482.2637-0.09510.51180.03350.00890.0816-0.0909-0.2342-0.43670.24330.32590.2675-0.50830.80510.38771.92930.8961-0.24071.28090.08921.402152.7752-16.876710.4748
490.3459-0.28480.95680.2295-0.78882.649-0.622-0.614-0.0270.56010.26970.3139-0.8052-0.79050.40152.0559-0.12910.31012.43280.3491.285656.5327-27.013513.7424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'B' AND (RESID 512 THROUGH 546 )
2X-RAY DIFFRACTION2CHAIN 'B' AND (RESID 547 THROUGH 569 )
3X-RAY DIFFRACTION3CHAIN 'B' AND (RESID 570 THROUGH 596 )
4X-RAY DIFFRACTION4CHAIN 'B' AND (RESID 597 THROUGH 611 )
5X-RAY DIFFRACTION5CHAIN 'B' AND (RESID 612 THROUGH 638 )
6X-RAY DIFFRACTION6CHAIN 'B' AND (RESID 639 THROUGH 665 )
7X-RAY DIFFRACTION7CHAIN 'D' AND (RESID 1 THROUGH 44 )
8X-RAY DIFFRACTION8CHAIN 'D' AND (RESID 45 THROUGH 124 )
9X-RAY DIFFRACTION9CHAIN 'D' AND (RESID 125 THROUGH 153 )
10X-RAY DIFFRACTION10CHAIN 'D' AND (RESID 154 THROUGH 242 )
11X-RAY DIFFRACTION11CHAIN 'E' AND (RESID 2 THROUGH 106A)
12X-RAY DIFFRACTION12CHAIN 'E' AND (RESID 107 THROUGH 144 )
13X-RAY DIFFRACTION13CHAIN 'E' AND (RESID 145 THROUGH 179 )
14X-RAY DIFFRACTION14CHAIN 'E' AND (RESID 180 THROUGH 210 )
15X-RAY DIFFRACTION15CHAIN 'G' AND (RESID 31 THROUGH 117 )
16X-RAY DIFFRACTION16CHAIN 'G' AND (RESID 118 THROUGH 168 )
17X-RAY DIFFRACTION17CHAIN 'G' AND (RESID 169 THROUGH 203 )
18X-RAY DIFFRACTION18CHAIN 'G' AND (RESID 204 THROUGH 300 )
19X-RAY DIFFRACTION19CHAIN 'G' AND (RESID 301 THROUGH 373 )
20X-RAY DIFFRACTION20CHAIN 'G' AND (RESID 374 THROUGH 412 )
21X-RAY DIFFRACTION21CHAIN 'G' AND (RESID 413 THROUGH 457 )
22X-RAY DIFFRACTION22CHAIN 'G' AND (RESID 458 THROUGH 510)
23X-RAY DIFFRACTION23CHAIN 'H' AND (RESID 1 THROUGH 33 )
24X-RAY DIFFRACTION24CHAIN 'H' AND (RESID 34 THROUGH 45 )
25X-RAY DIFFRACTION25CHAIN 'H' AND (RESID 46 THROUGH 59 )
26X-RAY DIFFRACTION26CHAIN 'H' AND (RESID 60 THROUGH 100P)
27X-RAY DIFFRACTION27CHAIN 'H' AND (RESID 100Q THROUGH 122 )
28X-RAY DIFFRACTION28CHAIN 'H' AND (RESID 123 THROUGH 211 )
29X-RAY DIFFRACTION29CHAIN 'L' AND (RESID 6 THROUGH 99 )
30X-RAY DIFFRACTION30CHAIN 'L' AND (RESID 100 THROUGH 116 )
31X-RAY DIFFRACTION31CHAIN 'L' AND (RESID 117 THROUGH 172 )
32X-RAY DIFFRACTION32CHAIN 'L' AND (RESID 173 THROUGH 210 )
33X-RAY DIFFRACTION33CHAIN 'U' AND (RESID 1 THROUGH 6 )
34X-RAY DIFFRACTION34CHAIN 'U' AND (RESID 7 THROUGH 18 )
35X-RAY DIFFRACTION35CHAIN 'U' AND (RESID 19 THROUGH 36 )
36X-RAY DIFFRACTION36CHAIN 'U' AND (RESID 37 THROUGH 48 )
37X-RAY DIFFRACTION37CHAIN 'U' AND (RESID 49 THROUGH 55 )
38X-RAY DIFFRACTION38CHAIN 'U' AND (RESID 56 THROUGH 66 )
39X-RAY DIFFRACTION39CHAIN 'U' AND (RESID 67 THROUGH 82 )
40X-RAY DIFFRACTION40CHAIN 'U' AND (RESID 82A THROUGH 91 )
41X-RAY DIFFRACTION41CHAIN 'U' AND (RESID 92 THROUGH 99 )
42X-RAY DIFFRACTION42CHAIN 'U' AND (RESID 100 THROUGH 111 )
43X-RAY DIFFRACTION43CHAIN 'V' AND (RESID 3 THROUGH 23 )
44X-RAY DIFFRACTION44CHAIN 'V' AND (RESID 24 THROUGH 38 )
45X-RAY DIFFRACTION45CHAIN 'V' AND (RESID 39 THROUGH 48 )
46X-RAY DIFFRACTION46CHAIN 'V' AND (RESID 49 THROUGH 62 )
47X-RAY DIFFRACTION47CHAIN 'V' AND (RESID 63 THROUGH 75 )
48X-RAY DIFFRACTION48CHAIN 'V' AND (RESID 76 THROUGH 101 )
49X-RAY DIFFRACTION49CHAIN 'V' AND (RESID 102 THROUGH 106 )

+
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://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