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- PDB-4hg4: Crystal structure of Fab 2G1 in complex with a H2N2 influenza vir... -

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Basic information

Entry
Database: PDB / ID: 4hg4
TitleCrystal structure of Fab 2G1 in complex with a H2N2 influenza virus hemagglutinin
Components
  • (Hemagglutinin ...) x 2
  • Fab 2G1 heavy chain
  • Fab 2G1 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / 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 / membrane
Similarity search - Function
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 ...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
Hemagglutinin / Hemagglutinin
Similarity search - Component
Biological speciesInfluenza A virus
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsXu, R. / Wilson, I.A.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2013
Title: A recurring motif for antibody recognition of the receptor-binding site of influenza hemagglutinin.
Authors: Xu, R. / Krause, J.C. / McBride, R. / Paulson, J.C. / Crowe, J.E. / Wilson, I.A.
History
DepositionOct 6, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2013Provider: repository / Type: Initial release
Revision 1.1May 22, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _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.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 / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Hemagglutinin HA1
a: Hemagglutinin HA2
B: Hemagglutinin HA1
b: Hemagglutinin HA2
C: Hemagglutinin HA1
c: Hemagglutinin HA2
D: Hemagglutinin HA1
d: Hemagglutinin HA2
E: Hemagglutinin HA1
e: Hemagglutinin HA2
F: Hemagglutinin HA1
f: Hemagglutinin HA2
G: Hemagglutinin HA1
g: Hemagglutinin HA2
H: Hemagglutinin HA1
h: Hemagglutinin HA2
I: Hemagglutinin HA1
i: Hemagglutinin HA2
J: Fab 2G1 heavy chain
K: Fab 2G1 light chain
L: Fab 2G1 heavy chain
M: Fab 2G1 light chain
N: Fab 2G1 heavy chain
O: Fab 2G1 light chain
P: Fab 2G1 heavy chain
Q: Fab 2G1 light chain
R: Fab 2G1 heavy chain
S: Fab 2G1 light chain
T: Fab 2G1 heavy chain
U: Fab 2G1 light chain
V: Fab 2G1 heavy chain
W: Fab 2G1 light chain
X: Fab 2G1 heavy chain
Y: Fab 2G1 light chain
Z: Fab 2G1 heavy chain
z: Fab 2G1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)939,77251
Polymers933,89436
Non-polymers5,87815
Water0
1
A: Hemagglutinin HA1
a: Hemagglutinin HA2
B: Hemagglutinin HA1
b: Hemagglutinin HA2
C: Hemagglutinin HA1
c: Hemagglutinin HA2
J: Fab 2G1 heavy chain
K: Fab 2G1 light chain
L: Fab 2G1 heavy chain
M: Fab 2G1 light chain
N: Fab 2G1 heavy chain
O: Fab 2G1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,17617
Polymers311,29812
Non-polymers1,8785
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: Hemagglutinin HA1
d: Hemagglutinin HA2
E: Hemagglutinin HA1
e: Hemagglutinin HA2
F: Hemagglutinin HA1
f: Hemagglutinin HA2
P: Fab 2G1 heavy chain
Q: Fab 2G1 light chain
R: Fab 2G1 heavy chain
S: Fab 2G1 light chain
T: Fab 2G1 heavy chain
U: Fab 2G1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,01417
Polymers311,29812
Non-polymers1,7165
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: Hemagglutinin HA1
g: Hemagglutinin HA2
H: Hemagglutinin HA1
h: Hemagglutinin HA2
I: Hemagglutinin HA1
i: Hemagglutinin HA2
V: Fab 2G1 heavy chain
W: Fab 2G1 light chain
X: Fab 2G1 heavy chain
Y: Fab 2G1 light chain
Z: Fab 2G1 heavy chain
z: Fab 2G1 light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)313,58217
Polymers311,29812
Non-polymers2,2845
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.842, 133.143, 812.990
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
11chain F and (resseq 20:53 or resseq 53:81 or resseq...
21chain G and (resseq 20:53 or resseq 53:81 or resseq...
31chain H and (resseq 20:53 or resseq 53:81 or resseq...
41chain I and (resseq 20:53 or resseq 53:81 or resseq...
12chain C and (resseq 10:53 or resseq 53:81 or resseq...
22chain D and (resseq 10:53 or resseq 53:81 or resseq...
32chain E and (resseq 10:53 or resseq 53:81 or resseq...
13chain A and (resseq 13:53 or resseq 53:81 or resseq...
23chain B and (resseq 13:53 or resseq 53:81 or resseq...
14chain c and (resseq 1:60 or resseq 66:172 )
24chain d and (resseq 1:60 or resseq 66:172 )
34chain e and (resseq 1:60 or resseq 66:172 )
44chain f and (resseq 1:60 or resseq 66:172 )
54chain g and (resseq 1:60 or resseq 66:172 )
64chain h and (resseq 1:60 or resseq 66:172 )
74chain i and (resseq 1:60 or resseq 66:172 )
15chain a and (resseq 1:60 or resseq 66:138 or resseq 144:171 )
25chain b and (resseq 1:60 or resseq 66:138 or resseq 144:171 )
16chain X and (resseq 2:52 or resseq 52:82 or resseq...
26chain Z and (resseq 2:52 or resseq 52:82 or resseq...
17chain V and (resseq 2:52 or resseq 52:82 or resseq...
27chain P and (resseq 2:52 or resseq 52:82 or resseq...
37chain R and (resseq 2:52 or resseq 52:82 or resseq...
47chain T and (resseq 2:52 or resseq 52:82 or resseq...
18chain z and (resseq 1:104 or resseq 156:165 or resseq 175:179 )
28chain Q and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )
38chain S and (resseq 1:153 or resseq 155:211 )
48chain U and (resseq 1:153 or resseq 155:211 )
58chain W and (resseq 1:105 )
68chain Y and (resseq 1:109 )
19chain M and (resseq 1:212 )
29chain O and (resseq 1:212 )
110chain L and (resseq 1:127 or resseq 136:213 )
210chain N and (resseq 1:127 or resseq 136:213 )

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F20 - 53
121chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F53 - 81
131chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F81 - 95
141chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F95 - 116
151chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F116
161chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F116
171chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F116 - 123
181chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F125 - 263
191chain 'F' and (resseq 20:53 or resseq 53:81 or resseq...F263 - 326
211chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G20 - 53
221chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G53 - 81
231chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G81 - 95
241chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G95 - 116
251chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G116
261chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G116
271chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G116 - 123
281chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G125 - 263
291chain 'G' and (resseq 20:53 or resseq 53:81 or resseq...G263 - 326
311chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H20 - 53
321chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H53 - 81
331chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H81 - 95
341chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H95 - 116
351chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H116
361chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H116
371chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H116 - 123
381chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H125 - 263
391chain 'H' and (resseq 20:53 or resseq 53:81 or resseq...H263 - 326
411chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I20 - 53
421chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I53 - 81
431chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I81 - 95
441chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I95 - 116
451chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I116
461chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I116
471chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I116 - 123
481chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I125 - 263
491chain 'I' and (resseq 20:53 or resseq 53:81 or resseq...I263 - 326
112chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C10 - 53
122chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C53 - 81
132chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C81 - 95
142chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C95 - 116
152chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C116
162chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C116
172chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C116 - 123
182chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C125 - 263
192chain 'C' and (resseq 10:53 or resseq 53:81 or resseq...C263 - 326
212chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D10 - 53
222chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D53 - 81
232chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D81 - 95
242chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D95 - 116
252chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D116
262chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D116
272chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D116 - 123
282chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D125 - 263
292chain 'D' and (resseq 10:53 or resseq 53:81 or resseq...D263 - 326
312chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E10 - 53
322chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E53 - 81
332chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E81 - 95
342chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E95 - 116
352chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E116
362chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E116
372chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E116 - 123
382chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E125 - 263
392chain 'E' and (resseq 10:53 or resseq 53:81 or resseq...E263 - 325
113chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A13 - 53
123chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A53 - 81
133chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A81 - 95
143chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A95 - 116
153chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A116
163chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A116
173chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A116 - 123
183chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A125 - 263
193chain 'A' and (resseq 13:53 or resseq 53:81 or resseq...A263 - 325
213chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B13 - 53
223chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B53 - 81
233chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B81 - 95
243chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B95 - 116
253chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B116
263chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B116
273chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B116 - 123
283chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B125 - 263
293chain 'B' and (resseq 13:53 or resseq 53:81 or resseq...B263 - 325
114chain 'c' and (resseq 1:60 or resseq 66:172 )c1 - 60
124chain 'c' and (resseq 1:60 or resseq 66:172 )c66 - 172
214chain 'd' and (resseq 1:60 or resseq 66:172 )d1 - 60
224chain 'd' and (resseq 1:60 or resseq 66:172 )d66 - 172
314chain 'e' and (resseq 1:60 or resseq 66:172 )e1 - 60
324chain 'e' and (resseq 1:60 or resseq 66:172 )e66 - 172
414chain 'f' and (resseq 1:60 or resseq 66:172 )f1 - 60
424chain 'f' and (resseq 1:60 or resseq 66:172 )f66 - 172
514chain 'g' and (resseq 1:60 or resseq 66:172 )g1 - 60
524chain 'g' and (resseq 1:60 or resseq 66:172 )g66 - 172
614chain 'h' and (resseq 1:60 or resseq 66:172 )h1 - 60
624chain 'h' and (resseq 1:60 or resseq 66:172 )h66 - 172
714chain 'i' and (resseq 1:60 or resseq 66:172 )i1 - 60
724chain 'i' and (resseq 1:60 or resseq 66:172 )i66 - 172
115chain 'a' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )a1 - 60
125chain 'a' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )a66 - 138
135chain 'a' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )a144 - 171
215chain 'b' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )b1 - 60
225chain 'b' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )b66 - 138
235chain 'b' and (resseq 1:60 or resseq 66:138 or resseq 144:171 )b144 - 171
116chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X2 - 52
126chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X52 - 82
136chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X82
146chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X82
156chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X82 - 100
166chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X100
176chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X100
186chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X100 - 120
196chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X141 - 150
1106chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X165 - 179
1116chain 'X' and (resseq 2:52 or resseq 52:82 or resseq...X197 - 205
216chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z2 - 52
226chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z52 - 82
236chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z82
246chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z82
256chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z82 - 100
266chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z100
276chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z100
286chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z100 - 120
296chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z141 - 150
2106chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z165 - 179
2116chain 'Z' and (resseq 2:52 or resseq 52:82 or resseq...Z197 - 205
117chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V2 - 52
127chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V52 - 82
137chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V82
147chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V82
157chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V82 - 100
167chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V100
177chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V100
187chain 'V' and (resseq 2:52 or resseq 52:82 or resseq...V100 - 111
217chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P2 - 52
227chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P52 - 82
237chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P82
247chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P82
257chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P82 - 100
267chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P100
277chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P100
287chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P100 - 119
297chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P142 - 148
2107chain 'P' and (resseq 2:52 or resseq 52:82 or resseq...P154 - 181
317chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R2 - 52
327chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R52 - 82
337chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R82
347chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R82
357chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R82 - 100
367chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R100
377chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R100
387chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R100 - 126
397chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R137 - 184
3107chain 'R' and (resseq 2:52 or resseq 52:82 or resseq...R188 - 213
417chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T2 - 52
427chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T52 - 82
437chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T82
447chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T82
457chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T82 - 100
467chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T100
477chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T100
487chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T100 - 126
497chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T137 - 184
4107chain 'T' and (resseq 2:52 or resseq 52:82 or resseq...T188 - 213
118chain 'z' and (resseq 1:104 or resseq 156:165 or resseq 175:179 )z1 - 104
128chain 'z' and (resseq 1:104 or resseq 156:165 or resseq 175:179 )z156 - 165
138chain 'z' and (resseq 1:104 or resseq 156:165 or resseq 175:179 )z175 - 179
218chain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )Q1 - 116
228chain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )Q132 - 144
238chain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )Q160 - 178
248chain 'Q' and (resseq 1:116 or resseq 132:144 or resseq 160:178 or resseq 196:204 )Q196 - 204
318chain 'S' and (resseq 1:153 or resseq 155:211 )S1 - 153
328chain 'S' and (resseq 1:153 or resseq 155:211 )S155 - 211
418chain 'U' and (resseq 1:153 or resseq 155:211 )U1 - 153
428chain 'U' and (resseq 1:153 or resseq 155:211 )U155 - 211
518chain 'W' and (resseq 1:105 )W1 - 105
618chain 'Y' and (resseq 1:109 )Y1 - 109
119chain 'M' and (resseq 1:212 )M1 - 212
219chain 'O' and (resseq 1:212 )O1 - 212
1110chain 'L' and (resseq 1:127 or resseq 136:213 )L1 - 127
1210chain 'L' and (resseq 1:127 or resseq 136:213 )L136 - 213
2110chain 'N' and (resseq 1:127 or resseq 136:213 )N1 - 127
2210chain 'N' and (resseq 1:127 or resseq 136:213 )N136 - 213

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10

NCS oper:
IDCodeMatrixVector
1given(-0.685079, -0.708405, -0.169792), (-0.636123, 0.468175, 0.613319), (-0.354986, 0.528181, -0.771369)-83.4879, 71.164703, -105.677002
2given(0.882724, -0.0446, -0.46777), (-0.009101, -0.996921, 0.077879), (-0.469803, -0.064489, -0.880412)-98.588402, -8.03648, -127.136002
3given(-0.41806, 0.902517, 0.103387), (0.904416, 0.402839, 0.140544), (0.085195, 0.152261, -0.984662)-27.149099, 24.132601, -132.906998
4given(-0.87393, 0.225282, 0.43069), (-0.414235, -0.808767, -0.417499), (0.254273, -0.543272, 0.800126)-108.667, 3.50978, -124.552002
5given(0.798859, 0.556833, 0.227511), (-0.584303, 0.808189, 0.073623), (-0.142876, -0.19175, 0.970988)-28.027599, 9.10435, -140.044998
6given(-0.408498, -0.912223, 0.031266), (0.76146, -0.359474, -0.539404), (0.503297, -0.196538, 0.841466)-68.831902, 22.6838, 20.3692
7given(-0.884297, 0.202418, 0.420768), (-0.391423, -0.81268, -0.431671), (0.254571, -0.546423, 0.797881)-109.956001, 4.30507, -124.657997
8given(0.786228, 0.573162, 0.230936), (-0.597413, 0.800555, 0.047005), (-0.157935, -0.17492, 0.971833)-29.214899, 8.20693, -140.514008
9given(0.214629, -0.971708, -0.098579), (0.904665, 0.235826, -0.354919), (0.368125, -0.013005, 0.929685)-68.733597, 73.118301, -114.931999
10given(0.484245, -0.712645, -0.507586), (-0.66758, -0.675948, 0.312141), (-0.565548, 0.187701, -0.803071)-140.856995, 57.519199, -246.906998
11given(0.316778, 0.944854, -0.083079), (0.944686, -0.322138, -0.061607), (-0.084972, -0.058967, -0.994637)-69.362801, 29.304001, -269.437012
12given(-0.993116, -0.109597, 0.041331), (-0.076378, 0.873455, 0.480876), (-0.088803, 0.47441, -0.875814)-78.020401, 102.115997, -248.311005
13given(-0.432813, -0.900289, 0.046387), (0.748172, -0.387436, -0.538639), (0.502903, -0.198425, 0.841259)-68.783401, 22.3314, 20.422701
14given(-0.428318, 0.700086, 0.571334), (-0.865807, -0.498957, -0.03768), (0.258692, -0.510804, 0.819852)66.806702, -32.628601, -27.302799
15given(-0.239992, 0.970602, -0.018331), (0.959981, 0.240089, 0.144202), (0.144364, 0.01701, -0.989378)-17.6532, 36.041698, -130.356995
16given(0.81577, -0.205191, -0.540755), (-0.240582, -0.970614, 0.005366), (-0.525965, 0.125719, -0.841163)21.4251, -30.923401, -161.098007
17given(-0.699382, -0.631457, -0.334853), (-0.685957, 0.461362, 0.56268), (-0.20082, 0.623223, -0.75582)-48.256199, -33.488499, -139.414993
18given(0.88285, -0.052921, -0.466664), (-0.093561, -0.993533, -0.064332), (-0.460242, 0.100457, -0.882092)26.3806, -23.048401, -156.785004
19given(-0.709319, -0.613053, -0.347896), (-0.695726, 0.529578, 0.485296), (-0.113275, 0.58627, -0.802157)-53.5229, -37.121201, -136.470993
20given(-0.490914, 0.869646, 0.052145), (0.868769, 0.484187, 0.103935), (0.065138, 0.096326, -0.993216)-26.819401, 28.2796, -132.563995
21given(-0.208026, 0.761349, 0.614063), (-0.956108, -0.290726, 0.036557), (0.206356, -0.579506, 0.78841)73.033997, -20.9161, -30.422501
22given(-0.406992, -0.885792, 0.223003), (0.708037, -0.460173, -0.535653), (0.577097, -0.060112, 0.81446)3.04171, -77.212303, -18.746799
23given(-0.450548, -0.890759, 0.059625), (0.75315, -0.415106, -0.510345), (0.479345, -0.185028, 0.8579)-70.828201, 29.440001, 21.8832
24given(-0.42756, -0.9023, 0.055197), (0.78096, -0.399435, -0.48016), (0.455296, -0.162191, 0.875442)-67.821701, 37.194901, 20.927999

-
Components

-
Hemagglutinin ... , 2 types, 18 molecules ABCDEFGHIabcdefghi

#1: Protein
Hemagglutinin HA1


Mass: 36573.379 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305+/1957(H2N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q67085, UniProt: P03451*PLUS
#2: Protein
Hemagglutinin HA2


Mass: 20139.295 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Influenza A virus / Strain: A/Japan/305+/1957(H2N2) / Gene: HA / Plasmid: pFastBac / Cell line (production host): Hi5 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q67085, UniProt: P03451*PLUS

-
Antibody , 2 types, 18 molecules JLNPRTVXZKMOQSUWYz

#3: Antibody
Fab 2G1 heavy chain


Mass: 23424.170 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEE6.4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)
#4: Antibody
Fab 2G1 light chain


Mass: 23629.189 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEE12.4 / Cell line (production host): HEK 293F / Production host: Homo sapiens (human)

-
Sugars , 3 types, 15 molecules

#5: 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
#6: 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.: 2
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
#7: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4
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

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.67 Å3/Da / Density % sol: 66.5 %
Crystal growTemperature: 295.7 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 10% PEG6000, 0.1 M HEPES, pH 7.5, vapor diffusion, sitting drop, temperature 295.7K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 11, 2012
Details: Shutterless data collection; Fine phi slicing experiments
RadiationMonochromator: Liquid nitrogen-cooled double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionRedundancy: 6.6 % / Av σ(I) over netI: 11.53 / Number: 1549028 / Rmerge(I) obs: 0.133 / Χ2: 1.01 / D res high: 3.15 Å / D res low: 50 Å / Num. obs: 234983 / % possible obs: 98.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
6.785098.510.070.9616.6
5.386.7898.910.0890.9326.7
4.75.3899.810.11.0166.9
4.274.798.310.1141.0166.6
3.974.2799.810.1610.9986.9
3.733.9799.710.2471.0827
3.553.7397.710.3261.0926.5
3.393.5599.610.4711.016.7
3.263.3999.510.6450.946.4
3.153.2695.610.8191.0755.5
ReflectionResolution: 3.15→50 Å / Num. obs: 234983 / % possible obs: 98.7 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.133 / Net I/σ(I): 5.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.15-3.265.50.819195.6
3.26-3.396.40.645199.5
3.39-3.556.70.471199.6
3.55-3.736.50.326197.7
3.73-3.9770.247199.7
3.97-4.276.90.161199.8
4.27-4.76.60.114198.3
4.7-5.386.90.1199.8
5.38-6.786.70.089198.9
6.78-506.60.07198.5

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHENIX1.7.2_869refinement
PDB_EXTRACT3.11data extraction
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.2→48.13 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.99 / σ(F): 0 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3019 10333 5.02 %
Rwork0.249 --
obs0.2517 205778 90.25 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 23.003 Å2 / ksol: 0.286 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.7199 Å2-0 Å2-0 Å2
2---3.6156 Å20 Å2
3----7.4957 Å2
Refinement stepCycle: LAST / Resolution: 3.2→48.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms58356 0 386 0 58742
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0160150
X-RAY DIFFRACTIONf_angle_d1.36681619
X-RAY DIFFRACTIONf_dihedral_angle_d20.83822062
X-RAY DIFFRACTIONf_chiral_restr0.0888963
X-RAY DIFFRACTIONf_plane_restr0.00710484
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11F2458X-RAY DIFFRACTIONPOSITIONAL0.035
12G2458X-RAY DIFFRACTIONPOSITIONAL0.035
13H2458X-RAY DIFFRACTIONPOSITIONAL0.036
14I2458X-RAY DIFFRACTIONPOSITIONAL0.023
21C2532X-RAY DIFFRACTIONPOSITIONAL0.041
22D2532X-RAY DIFFRACTIONPOSITIONAL0.041
23E2524X-RAY DIFFRACTIONPOSITIONAL0.05
31A2503X-RAY DIFFRACTIONPOSITIONAL0.036
32B2503X-RAY DIFFRACTIONPOSITIONAL0.036
41c1355X-RAY DIFFRACTIONPOSITIONAL0.029
42d1355X-RAY DIFFRACTIONPOSITIONAL0.029
43e1355X-RAY DIFFRACTIONPOSITIONAL0.033
44f1355X-RAY DIFFRACTIONPOSITIONAL0.041
45g1355X-RAY DIFFRACTIONPOSITIONAL0.029
46h1355X-RAY DIFFRACTIONPOSITIONAL0.03
47i1355X-RAY DIFFRACTIONPOSITIONAL0.033
51a1295X-RAY DIFFRACTIONPOSITIONAL0.032
52b1295X-RAY DIFFRACTIONPOSITIONAL0.032
61X1204X-RAY DIFFRACTIONPOSITIONAL0.024
62Z1204X-RAY DIFFRACTIONPOSITIONAL0.024
71V883X-RAY DIFFRACTIONPOSITIONAL0.028
72P883X-RAY DIFFRACTIONPOSITIONAL0.028
73R883X-RAY DIFFRACTIONPOSITIONAL0.02
74T883X-RAY DIFFRACTIONPOSITIONAL0.018
81z883X-RAY DIFFRACTIONPOSITIONAL0.037
82Q883X-RAY DIFFRACTIONPOSITIONAL0.037
83S915X-RAY DIFFRACTIONPOSITIONAL0.04
84U915X-RAY DIFFRACTIONPOSITIONAL0.036
85W809X-RAY DIFFRACTIONPOSITIONAL0.033
86Y809X-RAY DIFFRACTIONPOSITIONAL0.023
91M1646X-RAY DIFFRACTIONPOSITIONAL0.051
92O1646X-RAY DIFFRACTIONPOSITIONAL0.051
101L1578X-RAY DIFFRACTIONPOSITIONAL0.05
102N1578X-RAY DIFFRACTIONPOSITIONAL0.05
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2-3.23640.3956570.36151077X-RAY DIFFRACTION15
3.2364-3.27440.4125980.35211915X-RAY DIFFRACTION27
3.2744-3.31440.38351380.3332975X-RAY DIFFRACTION42
3.3144-3.35630.38232320.33134554X-RAY DIFFRACTION64
3.3563-3.40040.40543030.32626048X-RAY DIFFRACTION84
3.4004-3.4470.37473680.32486962X-RAY DIFFRACTION98
3.447-3.49620.34043800.31587122X-RAY DIFFRACTION100
3.4962-3.54840.35133830.31177116X-RAY DIFFRACTION100
3.5484-3.60380.373580.29867203X-RAY DIFFRACTION100
3.6038-3.66290.36953900.29257032X-RAY DIFFRACTION100
3.6629-3.72610.34113330.27966831X-RAY DIFFRACTION95
3.7261-3.79380.34493650.2747024X-RAY DIFFRACTION99
3.7938-3.86670.32563920.26857143X-RAY DIFFRACTION100
3.8667-3.94560.32443750.27127161X-RAY DIFFRACTION100
3.9456-4.03140.32044020.23447155X-RAY DIFFRACTION100
4.0314-4.12510.28433470.23627165X-RAY DIFFRACTION100
4.1251-4.22820.26773890.22687204X-RAY DIFFRACTION100
4.2282-4.34240.26384200.21937130X-RAY DIFFRACTION100
4.3424-4.47010.25113860.20677177X-RAY DIFFRACTION100
4.4701-4.61430.2613720.20956884X-RAY DIFFRACTION96
4.6143-4.77910.28713790.20537147X-RAY DIFFRACTION99
4.7791-4.97020.254300.2017194X-RAY DIFFRACTION100
4.9702-5.19620.26213660.20477202X-RAY DIFFRACTION100
5.1962-5.46980.24883890.22117235X-RAY DIFFRACTION100
5.4698-5.8120.2973790.23867293X-RAY DIFFRACTION100
5.812-6.25980.32923490.24427042X-RAY DIFFRACTION97
6.2598-6.88810.28963950.23237295X-RAY DIFFRACTION100
6.8881-7.88110.27413810.21577397X-RAY DIFFRACTION100
7.8811-9.91510.24723810.20267252X-RAY DIFFRACTION98
9.9151-48.13530.32323960.28847510X-RAY DIFFRACTION97
Refinement TLS params.Method: refined / Origin x: -48.7637 Å / Origin y: 13.0626 Å / Origin z: -109.0588 Å
111213212223313233
T0.1315 Å20.1082 Å2-0.0705 Å2-0.1323 Å20.0842 Å2--0.035 Å2
L-0.0944 °2-0.0695 °20.1271 °2--0.166 °2-0.2166 °2---0.0462 °2
S0.0458 Å °-0.2421 Å °-0.0413 Å °0.2168 Å °0.0394 Å °-0.0279 Å °0.0945 Å °0.0751 Å °0.0829 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA8 - 325
2X-RAY DIFFRACTION1alla1 - 171
3X-RAY DIFFRACTION1allB13 - 325
4X-RAY DIFFRACTION1allb1 - 172
5X-RAY DIFFRACTION1allC9 - 326
6X-RAY DIFFRACTION1allc1 - 172
7X-RAY DIFFRACTION1allD9 - 326
8X-RAY DIFFRACTION1alld1 - 172
9X-RAY DIFFRACTION1allE8 - 325
10X-RAY DIFFRACTION1alle1 - 172
11X-RAY DIFFRACTION1allF9 - 326
12X-RAY DIFFRACTION1allf1 - 172
13X-RAY DIFFRACTION1allG9 - 326
14X-RAY DIFFRACTION1allg1 - 172
15X-RAY DIFFRACTION1allH9 - 327
16X-RAY DIFFRACTION1allh1 - 172
17X-RAY DIFFRACTION1allI9 - 326
18X-RAY DIFFRACTION1alli1 - 172
19X-RAY DIFFRACTION1allJ1 - 108
20X-RAY DIFFRACTION1allK1 - 106
21X-RAY DIFFRACTION1allL1 - 213
22X-RAY DIFFRACTION1allM1 - 214
23X-RAY DIFFRACTION1allN1 - 216
24X-RAY DIFFRACTION1allO1 - 214
25X-RAY DIFFRACTION1allP1 - 181
26X-RAY DIFFRACTION1allQ1 - 204
27X-RAY DIFFRACTION1allR1 - 213
28X-RAY DIFFRACTION1allS1 - 211
29X-RAY DIFFRACTION1allT2 - 213
30X-RAY DIFFRACTION1allU1 - 211
31X-RAY DIFFRACTION1allV2 - 111
32X-RAY DIFFRACTION1allW1 - 105
33X-RAY DIFFRACTION1allX2 - 207
34X-RAY DIFFRACTION1allY1 - 109
35X-RAY DIFFRACTION1allZ1 - 205
36X-RAY DIFFRACTION1allz1 - 179
37X-RAY DIFFRACTION1allH - E101 - 403

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