[English] 日本語
Yorodumi
- PDB-6b3m: The crystal structure of a broadly-reactive human anti-hemaggluti... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6b3m
TitleThe crystal structure of a broadly-reactive human anti-hemagglutinin stalk antibody (70-1F02) in complex with H5 hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • 70-1F02 Fab Heavy Chain
  • 70-1F02 Fab Light Chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / antibody / hemagglutinin / influenza / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


viral budding from plasma membrane / clathrin-dependent endocytosis of virus by host cell / host cell surface receptor binding / apical plasma membrane / 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 / identical protein binding
Similarity search - Function
Haemagglutinin, influenzavirus B / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin ...Haemagglutinin, influenzavirus B / Hemagglutinin; Chain A, domain 2 / Hemagglutinin Chain A, Domain 2 / Hemagglutinin Ectodomain; Chain B - #10 / Hemagglutinin Ectodomain; Chain B / Hemagglutinin (Ha1 Chain); Chain: A; domain 1 / Haemagglutinin, alpha/beta domain, HA1 chain / Haemagglutinin, influenzavirus A / Haemagglutinin, HA1 chain, alpha/beta domain superfamily / Haemagglutinin / Haemagglutinin, influenzavirus A/B / Viral capsid/haemagglutinin protein / Ribbon / Immunoglobulins / Alpha-Beta Complex / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-D-mannopyranose / Hemagglutinin HA2 / Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesunidentified influenza virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.92 Å
AuthorsShore, D.A. / Yang, H. / Stevens, J.
CitationJournal: J. Virol. / Year: 2018
Title: Broadly Reactive Human Monoclonal Antibodies Elicited following Pandemic H1N1 Influenza Virus Exposure Protect Mice against Highly Pathogenic H5N1 Challenge.
Authors: Nachbagauer, R. / Shore, D. / Yang, H. / Johnson, S.K. / Gabbard, J.D. / Tompkins, S.M. / Wrammert, J. / Wilson, P.C. / Stevens, J. / Ahmed, R. / Krammer, F. / Ellebedy, A.H.
History
DepositionSep 22, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Aug 15, 2018Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
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 / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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 / _database_PDB_caveat.text / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: 70-1F02 Fab Heavy Chain
E: Hemagglutinin HA1
F: Hemagglutinin HA2
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: 70-1F02 Fab Heavy Chain
K: Hemagglutinin HA1
L: Hemagglutinin HA2
M: 70-1F02 Fab Heavy Chain
O: 70-1F02 Fab Heavy Chain
P: 70-1F02 Fab Light Chain
Q: Hemagglutinin HA1
R: Hemagglutinin HA2
S: Hemagglutinin HA1
T: Hemagglutinin HA2
V: 70-1F02 Fab Heavy Chain
Y: 70-1F02 Fab Heavy Chain
U: 70-1F02 Fab Light Chain
J: 70-1F02 Fab Light Chain
D: 70-1F02 Fab Light Chain
W: 70-1F02 Fab Light Chain
N: 70-1F02 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)645,83252
Polymers632,77924
Non-polymers13,05328
Water0
1
A: Hemagglutinin HA1
B: Hemagglutinin HA2
C: 70-1F02 Fab Heavy Chain
G: Hemagglutinin HA1
H: Hemagglutinin HA2
I: 70-1F02 Fab Heavy Chain
K: Hemagglutinin HA1
L: Hemagglutinin HA2
O: 70-1F02 Fab Heavy Chain
P: 70-1F02 Fab Light Chain
J: 70-1F02 Fab Light Chain
D: 70-1F02 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,21728
Polymers316,39012
Non-polymers6,82716
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
E: Hemagglutinin HA1
F: Hemagglutinin HA2
M: 70-1F02 Fab Heavy Chain
Q: Hemagglutinin HA1
R: Hemagglutinin HA2
Y: 70-1F02 Fab Heavy Chain
U: 70-1F02 Fab Light Chain
N: 70-1F02 Fab Light Chain
hetero molecules

S: Hemagglutinin HA1
T: Hemagglutinin HA2
V: 70-1F02 Fab Heavy Chain
W: 70-1F02 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)322,61524
Polymers316,39012
Non-polymers6,22612
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x+1/2,-y+1/2,-z1
Unit cell
Length a, b, c (Å)174.582, 205.368, 222.265
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12A
22G
13A
23K
14A
24Q
15A
25S
16B
26F
17B
27H
18B
28L
19B
29R
110B
210T
111C
211I
112C
212M
113C
213O
114C
214V
115C
215Y
116E
216G
117E
217K
118E
218Q
119E
219S
120F
220H
121F
221L
122F
222R
123F
223T
124G
224K
125G
225Q
126G
226S
127H
227L
128H
228R
129H
229T
130I
230M
131I
231O
132I
232V
133I
233Y
134K
234Q
135K
235S
136L
236R
137L
237T
138M
238O
139M
239V
140M
240Y
141O
241V
142O
242Y
143P
243U
144P
244J
145P
245D
146P
246W
147P
247N
148Q
248S
149R
249T
150V
250Y
151U
251J
152U
252D
153U
253W
154U
254N
155J
255D
156J
256W
157J
257N
158D
258W
159D
259N
160W
260N

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPPROPROAA1 - 3211 - 321
21ASPASPPROPROED1 - 3211 - 321
12ASPASPPROPROAA1 - 3211 - 321
22ASPASPPROPROGF1 - 3211 - 321
13ASPASPPROPROAA1 - 3211 - 321
23ASPASPPROPROKI1 - 3211 - 321
14ASPASPPROPROAA1 - 3211 - 321
24ASPASPPROPROQN1 - 3211 - 321
15ASPASPPROPROAA1 - 3211 - 321
25ASPASPPROPROSP1 - 3211 - 321
16GLYGLYILEILEBB1 - 1731 - 173
26GLYGLYILEILEFE1 - 1731 - 173
17GLYGLYILEILEBB1 - 1731 - 173
27GLYGLYILEILEHG1 - 1731 - 173
18GLYGLYILEILEBB1 - 1731 - 173
28GLYGLYILEILELJ1 - 1731 - 173
19GLYGLYILEILEBB1 - 1731 - 173
29GLYGLYILEILERO1 - 1731 - 173
110GLYGLYILEILEBB1 - 1731 - 173
210GLYGLYILEILETQ1 - 1731 - 173
111GLNGLNLYSLYSCC3 - 2213 - 221
211GLNGLNLYSLYSIH3 - 2213 - 221
112GLNGLNLYSLYSCC3 - 2213 - 221
212GLNGLNLYSLYSMK3 - 2213 - 221
113GLNGLNLYSLYSCC3 - 2213 - 221
213GLNGLNLYSLYSOL3 - 2213 - 221
114GLNGLNLYSLYSCC3 - 2213 - 221
214GLNGLNLYSLYSVR3 - 2213 - 221
115GLNGLNLYSLYSCC3 - 2213 - 221
215GLNGLNLYSLYSYS3 - 2213 - 221
116ASPASPPROPROED1 - 3211 - 321
216ASPASPPROPROGF1 - 3211 - 321
117ASPASPPROPROED1 - 3211 - 321
217ASPASPPROPROKI1 - 3211 - 321
118ASPASPPROPROED1 - 3211 - 321
218ASPASPPROPROQN1 - 3211 - 321
119ASPASPPROPROED1 - 3211 - 321
219ASPASPPROPROSP1 - 3211 - 321
120GLYGLYSERSERFE1 - 1751 - 175
220GLYGLYSERSERHG1 - 1751 - 175
121GLYGLYSERSERFE1 - 1751 - 175
221GLYGLYSERSERLJ1 - 1751 - 175
122GLYGLYSERSERFE1 - 1751 - 175
222GLYGLYSERSERRO1 - 1751 - 175
123GLYGLYSERSERFE1 - 1751 - 175
223GLYGLYSERSERTQ1 - 1751 - 175
124ASPASPPROPROGF1 - 3211 - 321
224ASPASPPROPROKI1 - 3211 - 321
125ASPASPPROPROGF1 - 3211 - 321
225ASPASPPROPROQN1 - 3211 - 321
126ASPASPPROPROGF1 - 3211 - 321
226ASPASPPROPROSP1 - 3211 - 321
127GLYGLYSERSERHG1 - 1751 - 175
227GLYGLYSERSERLJ1 - 1751 - 175
128GLYGLYSERSERHG1 - 1751 - 175
228GLYGLYSERSERRO1 - 1751 - 175
129GLYGLYSERSERHG1 - 1751 - 175
229GLYGLYSERSERTQ1 - 1751 - 175
130GLNGLNLYSLYSIH3 - 2213 - 221
230GLNGLNLYSLYSMK3 - 2213 - 221
131GLNGLNLYSLYSIH3 - 2213 - 221
231GLNGLNLYSLYSOL3 - 2213 - 221
132GLNGLNLYSLYSIH3 - 2213 - 221
232GLNGLNLYSLYSVR3 - 2213 - 221
133GLNGLNLYSLYSIH3 - 2213 - 221
233GLNGLNLYSLYSYS3 - 2213 - 221
134ASPASPPROPROKI1 - 3211 - 321
234ASPASPPROPROQN1 - 3211 - 321
135ASPASPPROPROKI1 - 3211 - 321
235ASPASPPROPROSP1 - 3211 - 321
136GLYGLYSERSERLJ1 - 1751 - 175
236GLYGLYSERSERRO1 - 1751 - 175
137GLYGLYSERSERLJ1 - 1751 - 175
237GLYGLYSERSERTQ1 - 1751 - 175
138GLNGLNLYSLYSMK3 - 2213 - 221
238GLNGLNLYSLYSOL3 - 2213 - 221
139GLNGLNLYSLYSMK3 - 2213 - 221
239GLNGLNLYSLYSVR3 - 2213 - 221
140GLNGLNLYSLYSMK3 - 2213 - 221
240GLNGLNLYSLYSYS3 - 2213 - 221
141GLNGLNLYSLYSOL3 - 2213 - 221
241GLNGLNLYSLYSVR3 - 2213 - 221
142GLNGLNLYSLYSOL3 - 2213 - 221
242GLNGLNLYSLYSYS3 - 2213 - 221
143ILEILEGLUGLUPM2 - 2132 - 214
243ILEILEGLUGLUUT2 - 2132 - 214
144ILEILEGLUGLUPM2 - 2132 - 214
244ILEILEGLUGLUJU2 - 2132 - 214
145ILEILEGLUGLUPM2 - 2132 - 214
245ILEILEGLUGLUDV2 - 2132 - 214
146ILEILEGLUGLUPM2 - 2132 - 214
246ILEILEGLUGLUWW2 - 2132 - 214
147ILEILEGLUGLUPM2 - 2132 - 214
247ILEILEGLUGLUNX2 - 2132 - 214
148ASPASPPROPROQN1 - 3211 - 321
248ASPASPPROPROSP1 - 3211 - 321
149GLYGLYSERSERRO1 - 1751 - 175
249GLYGLYSERSERTQ1 - 1751 - 175
150GLNGLNLYSLYSVR3 - 2213 - 221
250GLNGLNLYSLYSYS3 - 2213 - 221
151GLUGLUCYSCYSUT1 - 2141 - 215
251GLUGLUCYSCYSJU1 - 2141 - 215
152GLUGLUCYSCYSUT1 - 2141 - 215
252GLUGLUCYSCYSDV1 - 2141 - 215
153GLUGLUCYSCYSUT1 - 2141 - 215
253GLUGLUCYSCYSWW1 - 2141 - 215
154GLUGLUCYSCYSUT1 - 2141 - 215
254GLUGLUCYSCYSNX1 - 2141 - 215
155GLUGLUCYSCYSJU1 - 2141 - 215
255GLUGLUCYSCYSDV1 - 2141 - 215
156GLUGLUCYSCYSJU1 - 2141 - 215
256GLUGLUCYSCYSWW1 - 2141 - 215
157GLUGLUCYSCYSJU1 - 2141 - 215
257GLUGLUCYSCYSNX1 - 2141 - 215
158GLUGLUCYSCYSDV1 - 2141 - 215
258GLUGLUCYSCYSWW1 - 2141 - 215
159GLUGLUCYSCYSDV1 - 2141 - 215
259GLUGLUCYSCYSNX1 - 2141 - 215
160GLUGLUCYSCYSWW1 - 2141 - 215
260GLUGLUCYSCYSNX1 - 2141 - 215

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60

-
Components

-
Hemagglutinin ... , 2 types, 12 molecules AEGKQSBFHLRT

#1: Protein
Hemagglutinin HA1


Mass: 37607.688 Da / Num. of mol.: 6 / Fragment: UNP residues 17-346
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Gene: HA / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q5EP31, UniProt: Q6DQ33*PLUS
#2: Protein
Hemagglutinin HA2


Mass: 20881.104 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) unidentified influenza virus / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A0A182DWE1

-
Antibody , 2 types, 12 molecules CIMOVYPUJDWN

#3: Antibody
70-1F02 Fab Heavy Chain


Mass: 23534.408 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Antibody
70-1F02 Fab Light Chain


Mass: 23439.988 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)

-
Sugars , 8 types, 28 molecules

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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#6: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][a-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#7: 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.: 9
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
#8: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-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]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2-2-2/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#9: Polysaccharide alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[beta-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpb1-6]DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-2-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-L-Gulp]{}}}}}LINUCSPDB-CARE
#10: Polysaccharide beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...beta-D-mannopyranose-(1-4)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1122h-1b_1-5]/1-1-2-3/a4-b1_b4-c1_c4-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{[(4+1)][b-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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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
#12: Sugar ChemComp-BMA / beta-D-mannopyranose / beta-D-mannose / D-mannose / mannose / Mannose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-mannopyranoseCOMMON NAMEGMML 1.0
b-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 5.5
Details: 25% PEG3350, 200 mM sodium chloride, 100 mM Bis-Tris-HCl, pH 5.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: May 16, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.9→50 Å / Num. obs: 64141 / % possible obs: 98.8 % / Redundancy: 6.6 % / Net I/σ(I): 17.1
Reflection shellHighest resolution: 3.9 Å

-
Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2FK0

2fk0


Resolution: 3.92→50.01 Å / Cor.coef. Fo:Fc: 0.773 / Cor.coef. Fo:Fc free: 0.705 / SU B: 161.2 / SU ML: 0.946 / Cross valid method: THROUGHOUT / ESU R Free: 1.113 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32926 3422 5.1 %RANDOM
Rwork0.28626 ---
obs0.28842 64141 93.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 60.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2--0.53 Å20 Å2
3----0.5 Å2
Refinement stepCycle: 1 / Resolution: 3.92→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms43163 0 861 0 44024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01945136
X-RAY DIFFRACTIONr_bond_other_d0.0020.0239978
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.96661252
X-RAY DIFFRACTIONr_angle_other_deg2.475393484
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4155500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.65824.7612027
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.491157348
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.0215204
X-RAY DIFFRACTIONr_chiral_restr0.1030.26811
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02149664
X-RAY DIFFRACTIONr_gen_planes_other0.0040.028840
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it6.6396.22222126
X-RAY DIFFRACTIONr_mcbond_other6.646.22122125
X-RAY DIFFRACTIONr_mcangle_it11.5019.30827584
X-RAY DIFFRACTIONr_mcangle_other11.5019.30927585
X-RAY DIFFRACTIONr_scbond_it5.2316.21123010
X-RAY DIFFRACTIONr_scbond_other5.2316.21123010
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.449.29633662
X-RAY DIFFRACTIONr_long_range_B_refined15.80665.61746070
X-RAY DIFFRACTIONr_long_range_B_other15.80665.62146071
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A189680.01
12E189680.01
21A189820.01
22G189820.01
31A189420.01
32K189420.01
41A189820.02
42Q189820.02
51A189760.01
52S189760.01
61B101700.02
62F101700.02
71B101480.02
72H101480.02
81B101280.02
82L101280.02
91B101840.02
92R101840.02
101B101680.02
102T101680.02
111C114060.01
112I114060.01
121C114200.01
122M114200.01
131C114320.01
132O114320.01
141C114100.01
142V114100.01
151C114080.01
152Y114080.01
161E189800.01
162G189800.01
171E189720.01
172K189720.01
181E190020.02
182Q190020.02
191E190020.01
192S190020.01
201F102360.02
202H102360.02
211F102280.02
212L102280.02
221F102560.03
222R102560.03
231F102420.02
232T102420.02
241G189680.01
242K189680.01
251G190200.02
252Q190200.02
261G189960.01
262S189960.01
271H101980.02
272L101980.02
281H102500.02
282R102500.02
291H102180.03
292T102180.03
301I114080.01
302M114080.01
311I114200.01
312O114200.01
321I114000.01
322V114000.01
331I114000.01
332Y114000.01
341K189740.02
342Q189740.02
351K190240.01
352S190240.01
361L102180.03
362R102180.03
371L102160.02
372T102160.02
381M114200.01
382O114200.01
391M114080.01
392V114080.01
401M114080.01
402Y114080.01
411O114120.01
412V114120.01
421O114040.01
422Y114040.01
431P119560.01
432U119560.01
441P119580.01
442J119580.01
451P119680.01
452D119680.01
461P119500.01
462W119500.01
471P119520.01
472N119520.01
481Q189980.02
482S189980.02
491R102520.03
492T102520.03
501V113900.01
502Y113900.01
511U120340.01
512J120340.01
521U120340.01
522D120340.01
531U120340.01
532W120340.01
541U120260.01
542N120260.01
551J120120.01
552D120120.01
561J120140.01
562W120140.01
571J120040.01
572N120040.01
581D120320.01
582W120320.01
591D120380.01
592N120380.01
601W120280.01
602N120280.01
LS refinement shellResolution: 3.924→4.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 160 -
Rwork0.345 2682 -
obs--54.26 %
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)
10.7638-0.2907-1.06050.32140.09022.2782-0.109-0.01690.0267-0.0525-0.1262-0.16040.0658-0.06030.23530.57720.06420.10460.39610.01730.7701-7.973726.8941-21.5058
22.8949-1.4541-3.67530.94471.71944.79430.0021-0.2965-0.00290.02780.13780.0340.06230.317-0.13990.50650.03030.03290.7497-0.06020.5663-30.617632.980226.7912
30.15580.1279-0.32193.3398-2.14322.6376-0.1027-0.18950.0333-0.3654-0.06780.21690.02760.03020.17040.6328-0.0457-0.29130.5535-0.2020.6461-33.805665.4007-3.2515
41.6977-1.63690.51812.2814-0.65790.6465-0.04820.0150.0261-0.40540.05860.0086-0.34510.1148-0.01041.14990.0696-0.31120.173-0.11550.6162-11.8479114.214-6.0823
52.1063-3.18160.18855.1468-0.24310.235-0.1327-0.1744-0.1197-0.21520.14580.3343-0.06070.3137-0.01320.64140.13160.11510.6117-0.12420.731118.416975.919114.2255
60.7197-0.2806-1.18110.68910.5251.99760.0307-0.19340.03860.08350.024-0.5446-0.12020.1812-0.05470.27380.0578-0.04130.7665-0.09630.849420.513719.806-2.2936
71.2183-0.3571-2.26930.26870.53674.8606-0.07730.0024-0.28990.08830.04220.0630.1537-0.15740.03510.62480.05640.00430.71810.17450.5921-26.657113.969133.9498
81.79342.32760.74843.12820.99340.33450.06040.2553-0.18170.12170.0921-0.223-0.02320.0555-0.15250.6357-0.0222-0.37470.4994-0.02591.0395-41.7309-23.809114.8696
90.6866-0.214-1.06970.430.63132.41370.0911-0.0962-0.20380.08840.0486-0.25260.22670.0175-0.13970.56160.1847-0.03170.480.00340.7447-2.3972-5.7339-10.182
101.1298-1.0526-2.51611.16162.4596.1975-0.0605-0.0092-0.14860.24740.051-0.10930.0879-0.03180.00950.69060.0009-0.06290.70940.01310.461-13.857429.099237.9332
110.52380.48511.09310.61541.3833.1214-0.45440.0810.3-0.17580.06250.2152-0.4290.1490.39190.8006-0.1518-0.12680.4182-0.01950.8032-3.046669.289-25.2073
123.5706-0.78370.98880.2366-0.47371.57340.04950.21160.0284-0.0231-0.1275-0.02640.04720.05910.0780.7184-0.1527-0.26050.51680.26980.610129.12222.044245.7761
134.594-0.70260.80070.2829-0.59391.5635-0.051-0.4423-0.4409-0.06110.0082-0.0680.3985-0.08930.04280.6735-0.0569-0.2220.48720.27390.613330.36810.893460.1331
140.9852-1.35550.12772.2079-0.37190.6257-0.0189-0.103-0.2317-0.148-0.09090.2838-0.169-0.18080.10980.61840.1714-0.20840.4502-0.20760.8587-26.5678112.880226.2659
151.3657-2.28460.38594.0274-0.89021.2689-0.2108-0.15360.01540.07340.10260.11460.09480.40720.10820.55560.18680.01950.5635-0.01280.748110.161574.511833.0459
161.26591.3454-0.23971.5039-0.28031.11870.13520.1896-0.07830.25290.107-0.11830.76620.3043-0.24220.99220.123-0.03960.2483-0.21720.9031-85.5283-30.2918-20.154
174.03643.8966-1.70014.0335-1.64051.25480.1417-0.02310.29190.2788-0.08580.33860.14950.5283-0.05590.3573-0.0347-0.05290.8469-0.10370.7055-60.760216.413-29.4922
181.773-1.27420.47141.7564-0.12261.05230.58260.7699-0.4289-0.0971-0.64860.4420.6003-0.33840.0660.6822-0.0099-0.1920.6973-0.38330.6237-36.753-21.1731-26.4758
191.6944-0.2284-0.49030.43830.77121.39590.0531-0.6553-0.1269-0.0788-0.074-0.0125-0.12570.05260.02090.62570.18320.41830.93820.11590.664-19.888182.011265.3566
205.03260.8478-2.73720.764-0.14531.68810.3919-1.40730.39420.3159-0.20790.1843-0.16830.8825-0.1840.85290.2110.17551.1599-0.14490.077-10.692581.108381.2426
210.43930.3576-0.37563.20162.09142.50990.07730.0139-0.02260.1244-0.50390.590.2324-0.52980.42660.4564-0.0667-0.46320.658-0.15180.8624-60.1491-22.731814.137
220.31640.3608-0.52963.5009-1.67831.32990.2055-0.1903-0.05380.3823-0.32510.3715-0.52810.22910.11960.7369-0.1636-0.3840.5522-0.25150.6665-30.663480.80215.7811
230.9279-0.83150.77973.92091.46612.55240.13550.19690.20190.90830.0444-0.61670.7641-0.0816-0.17990.5810.0309-0.15230.4910.03510.6817-23.2046-18.0899-14.7952
241.7833-0.05351.23730.34660.36762.8572-0.19280.1076-0.2512-0.05450.11450.05540.2725-0.12890.07830.7607-0.1780.0210.2764-0.19720.722-10.228952.6136-24.0171
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 337
2X-RAY DIFFRACTION2B1 - 177
3X-RAY DIFFRACTION3C3 - 221
4X-RAY DIFFRACTION4E1 - 340
5X-RAY DIFFRACTION5F1 - 175
6X-RAY DIFFRACTION6G1 - 336
7X-RAY DIFFRACTION7H1 - 175
8X-RAY DIFFRACTION8I3 - 221
9X-RAY DIFFRACTION9K1 - 337
10X-RAY DIFFRACTION10L1 - 175
11X-RAY DIFFRACTION11M3 - 221
12X-RAY DIFFRACTION12O3 - 221
13X-RAY DIFFRACTION13P2 - 214
14X-RAY DIFFRACTION14Q1 - 337
15X-RAY DIFFRACTION15R1 - 177
16X-RAY DIFFRACTION16S1 - 341
17X-RAY DIFFRACTION17T1 - 175
18X-RAY DIFFRACTION18V3 - 221
19X-RAY DIFFRACTION19Y3 - 221
20X-RAY DIFFRACTION20U1 - 214
21X-RAY DIFFRACTION21J1 - 214
22X-RAY DIFFRACTION22D1 - 214
23X-RAY DIFFRACTION23W1 - 214
24X-RAY DIFFRACTION24N1 - 214

+
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