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- PDB-7k6v: Crystal Structure of Virus-like Particles of GII.4 Norovirus Hous... -

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Basic information

Entry
Database: PDB / ID: 7k6v
TitleCrystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus (HOV)
ComponentsCapsid protein VP1
KeywordsVIRUS LIKE PARTICLE / Norovirus / capsid protein / Houston virus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / : / VP1
Function and homology information
Biological speciesNorovirus Hu/Houston/TCH186/2002/US
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsHu, L. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 United States
CitationJournal: To Be Published
Title: Crystal structure of GII.4 Norovirus capsid reveals inherent conformational flexibility of the capsid protein
Authors: Hu, L. / Prasad, B.V.V.
History
DepositionSep 21, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,648,548118
Polymers2,644,24045
Non-polymers4,30873
Water543
1
AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
hetero molecules

AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
hetero molecules

AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
hetero molecules

AA: Capsid protein VP1
AB: Capsid protein VP1
AC: Capsid protein VP1
BA: Capsid protein VP1
BB: Capsid protein VP1
BC: Capsid protein VP1
CA: Capsid protein VP1
CB: Capsid protein VP1
CC: Capsid protein VP1
DA: Capsid protein VP1
DB: Capsid protein VP1
DC: Capsid protein VP1
EA: Capsid protein VP1
EB: Capsid protein VP1
EC: Capsid protein VP1
FA: Capsid protein VP1
FB: Capsid protein VP1
FC: Capsid protein VP1
GA: Capsid protein VP1
GB: Capsid protein VP1
GC: Capsid protein VP1
HA: Capsid protein VP1
HB: Capsid protein VP1
HC: Capsid protein VP1
IA: Capsid protein VP1
IB: Capsid protein VP1
IC: Capsid protein VP1
JA: Capsid protein VP1
JB: Capsid protein VP1
JC: Capsid protein VP1
KA: Capsid protein VP1
KB: Capsid protein VP1
KC: Capsid protein VP1
LA: Capsid protein VP1
LB: Capsid protein VP1
LC: Capsid protein VP1
MA: Capsid protein VP1
MB: Capsid protein VP1
MC: Capsid protein VP1
NA: Capsid protein VP1
NB: Capsid protein VP1
NC: Capsid protein VP1
OA: Capsid protein VP1
OB: Capsid protein VP1
OC: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,594,192472
Polymers10,576,961180
Non-polymers17,231292
Water21612
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation4_555x,-y,-z1
Unit cell
Length a, b, c (Å)420.170, 446.597, 463.952
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
31
41
51
61
71
81
91
101
111
121
131
141
151
161
171
181
191
201
211
221
231
241
251
261
271
281
291
301
311
321
331
341
351
361
371
381
391
401
411
421
431
441
451

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ALAALAARGARG(chain 'AA' and (resid 28 through 220 or (resid 221...AAA28 - 18728 - 187
12VALVALASNASN(chain 'AA' and (resid 28 through 220 or (resid 221...AAA195 - 302195 - 302
13ASNASNARGARG(chain 'AA' and (resid 28 through 220 or (resid 221...AAA310 - 435310 - 435
14CYSCYSALAALA(chain 'AA' and (resid 28 through 220 or (resid 221...AAA451 - 528451 - 528
21ALAALAARGARG(chain 'AB' and (resid 28 through 188 or resid 195...ABB28 - 18728 - 187
22VALVALASNASN(chain 'AB' and (resid 28 through 188 or resid 195...ABB195 - 302195 - 302
23ASNASNARGARG(chain 'AB' and (resid 28 through 188 or resid 195...ABB310 - 435310 - 435
24CYSCYSALAALA(chain 'AB' and (resid 28 through 188 or resid 195...ABB451 - 528451 - 528
31ALAALAARGARG(chain 'AC' and (resid 28 through 188 or resid 195...ACC28 - 18728 - 187
32VALVALASNASN(chain 'AC' and (resid 28 through 188 or resid 195...ACC195 - 302195 - 302
33ASNASNARGARG(chain 'AC' and (resid 28 through 188 or resid 195...ACC310 - 435310 - 435
34CYSCYSALAALA(chain 'AC' and (resid 28 through 188 or resid 195...ACC451 - 528451 - 528
41ALAALAARGARG(chain 'BA' and (resid 28 through 220 or (resid 221...BAD28 - 18728 - 187
42VALVALASNASN(chain 'BA' and (resid 28 through 220 or (resid 221...BAD195 - 302195 - 302
43ASNASNARGARG(chain 'BA' and (resid 28 through 220 or (resid 221...BAD310 - 435310 - 435
44CYSCYSALAALA(chain 'BA' and (resid 28 through 220 or (resid 221...BAD451 - 528451 - 528
51ALAALAARGARG(chain 'BB' and (resid 28 through 188 or resid 195...BBE28 - 18728 - 187
52VALVALASNASN(chain 'BB' and (resid 28 through 188 or resid 195...BBE195 - 302195 - 302
53ASNASNARGARG(chain 'BB' and (resid 28 through 188 or resid 195...BBE310 - 435310 - 435
54CYSCYSALAALA(chain 'BB' and (resid 28 through 188 or resid 195...BBE451 - 528451 - 528
61ALAALAARGARG(chain 'BC' and (resid 28 through 188 or resid 195...BCF28 - 18728 - 187
62VALVALASNASN(chain 'BC' and (resid 28 through 188 or resid 195...BCF195 - 302195 - 302
63ASNASNARGARG(chain 'BC' and (resid 28 through 188 or resid 195...BCF310 - 435310 - 435
64CYSCYSALAALA(chain 'BC' and (resid 28 through 188 or resid 195...BCF451 - 528451 - 528
71ALAALAARGARG(chain 'CA' and (resid 28 through 220 or (resid 221...CAG28 - 18728 - 187
72VALVALASNASN(chain 'CA' and (resid 28 through 220 or (resid 221...CAG195 - 302195 - 302
73ASNASNARGARG(chain 'CA' and (resid 28 through 220 or (resid 221...CAG310 - 435310 - 435
74CYSCYSALAALA(chain 'CA' and (resid 28 through 220 or (resid 221...CAG451 - 528451 - 528
81ALAALAARGARG(chain 'CB' and (resid 28 through 188 or resid 195...CBH28 - 18728 - 187
82VALVALASNASN(chain 'CB' and (resid 28 through 188 or resid 195...CBH195 - 302195 - 302
83ASNASNARGARG(chain 'CB' and (resid 28 through 188 or resid 195...CBH310 - 435310 - 435
84CYSCYSALAALA(chain 'CB' and (resid 28 through 188 or resid 195...CBH451 - 528451 - 528
91ALAALAARGARG(chain 'CC' and (resid 28 through 188 or resid 195...CCI28 - 18728 - 187
92VALVALASNASN(chain 'CC' and (resid 28 through 188 or resid 195...CCI195 - 302195 - 302
93ASNASNARGARG(chain 'CC' and (resid 28 through 188 or resid 195...CCI310 - 435310 - 435
94CYSCYSALAALA(chain 'CC' and (resid 28 through 188 or resid 195...CCI451 - 528451 - 528
101ALAALAARGARG(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ28 - 18728 - 187
102VALVALASNASN(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ195 - 302195 - 302
103ASNASNARGARG(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ310 - 435310 - 435
104CYSCYSALAALA(chain 'DA' and (resid 28 through 220 or (resid 221...DAJ451 - 528451 - 528
111ALAALAARGARG(chain 'DB' and (resid 28 through 188 or resid 195...DBK28 - 18728 - 187
112VALVALASNASN(chain 'DB' and (resid 28 through 188 or resid 195...DBK195 - 302195 - 302
113ASNASNARGARG(chain 'DB' and (resid 28 through 188 or resid 195...DBK310 - 435310 - 435
114CYSCYSALAALA(chain 'DB' and (resid 28 through 188 or resid 195...DBK451 - 528451 - 528
121ALAALAARGARG(chain 'DC' and (resid 28 through 188 or resid 195...DCL28 - 18728 - 187
122VALVALASNASN(chain 'DC' and (resid 28 through 188 or resid 195...DCL195 - 302195 - 302
123ASNASNARGARG(chain 'DC' and (resid 28 through 188 or resid 195...DCL310 - 435310 - 435
124CYSCYSALAALA(chain 'DC' and (resid 28 through 188 or resid 195...DCL451 - 528451 - 528
131ALAALAARGARG(chain 'EA' and (resid 28 through 220 or (resid 221...EAM28 - 18728 - 187
132VALVALASNASN(chain 'EA' and (resid 28 through 220 or (resid 221...EAM195 - 302195 - 302
133ASNASNARGARG(chain 'EA' and (resid 28 through 220 or (resid 221...EAM310 - 435310 - 435
134CYSCYSALAALA(chain 'EA' and (resid 28 through 220 or (resid 221...EAM451 - 528451 - 528
141ALAALAARGARG(chain 'EB' and (resid 28 through 188 or resid 195...EBN28 - 18728 - 187
142VALVALASNASN(chain 'EB' and (resid 28 through 188 or resid 195...EBN195 - 302195 - 302
143ASNASNARGARG(chain 'EB' and (resid 28 through 188 or resid 195...EBN310 - 435310 - 435
144CYSCYSALAALA(chain 'EB' and (resid 28 through 188 or resid 195...EBN451 - 528451 - 528
151ALAALAARGARG(chain 'EC' and (resid 28 through 188 or resid 195...ECO28 - 18728 - 187
152VALVALASNASN(chain 'EC' and (resid 28 through 188 or resid 195...ECO195 - 302195 - 302
153ASNASNARGARG(chain 'EC' and (resid 28 through 188 or resid 195...ECO310 - 435310 - 435
154CYSCYSALAALA(chain 'EC' and (resid 28 through 188 or resid 195...ECO451 - 528451 - 528
161ALAALAARGARG(chain 'FA' and (resid 28 through 220 or (resid 221...FAP28 - 18728 - 187
162VALVALASNASN(chain 'FA' and (resid 28 through 220 or (resid 221...FAP195 - 302195 - 302
163ASNASNARGARG(chain 'FA' and (resid 28 through 220 or (resid 221...FAP310 - 435310 - 435
164CYSCYSALAALA(chain 'FA' and (resid 28 through 220 or (resid 221...FAP451 - 528451 - 528
171ALAALAARGARG(chain 'FB' and (resid 28 through 188 or resid 195...FBQ28 - 18728 - 187
172VALVALASNASN(chain 'FB' and (resid 28 through 188 or resid 195...FBQ195 - 302195 - 302
173ASNASNARGARG(chain 'FB' and (resid 28 through 188 or resid 195...FBQ310 - 435310 - 435
174CYSCYSALAALA(chain 'FB' and (resid 28 through 188 or resid 195...FBQ451 - 528451 - 528
181ALAALAARGARG(chain 'FC' and (resid 28 through 188 or resid 195...FCR28 - 18728 - 187
182VALVALASNASN(chain 'FC' and (resid 28 through 188 or resid 195...FCR195 - 302195 - 302
183ASNASNARGARG(chain 'FC' and (resid 28 through 188 or resid 195...FCR310 - 435310 - 435
184CYSCYSALAALA(chain 'FC' and (resid 28 through 188 or resid 195...FCR451 - 528451 - 528
191ALAALAARGARG(chain 'GA' and (resid 28 through 220 or (resid 221...GAS28 - 18728 - 187
192VALVALASNASN(chain 'GA' and (resid 28 through 220 or (resid 221...GAS195 - 302195 - 302
193ASNASNARGARG(chain 'GA' and (resid 28 through 220 or (resid 221...GAS310 - 435310 - 435
194CYSCYSALAALA(chain 'GA' and (resid 28 through 220 or (resid 221...GAS451 - 528451 - 528
201ALAALAARGARG(chain 'GB' and (resid 28 through 188 or resid 195...GBT28 - 18728 - 187
202VALVALASNASN(chain 'GB' and (resid 28 through 188 or resid 195...GBT195 - 302195 - 302
203ASNASNARGARG(chain 'GB' and (resid 28 through 188 or resid 195...GBT310 - 435310 - 435
204CYSCYSALAALA(chain 'GB' and (resid 28 through 188 or resid 195...GBT451 - 528451 - 528
211ALAALAARGARG(chain 'GC' and (resid 28 through 188 or resid 195...GCU28 - 18728 - 187
212VALVALASNASN(chain 'GC' and (resid 28 through 188 or resid 195...GCU195 - 302195 - 302
213ASNASNARGARG(chain 'GC' and (resid 28 through 188 or resid 195...GCU310 - 435310 - 435
214CYSCYSALAALA(chain 'GC' and (resid 28 through 188 or resid 195...GCU451 - 528451 - 528
221ALAALAARGARG(chain 'HA' and (resid 28 through 220 or (resid 221...HAV28 - 18728 - 187
222VALVALASNASN(chain 'HA' and (resid 28 through 220 or (resid 221...HAV195 - 302195 - 302
223ASNASNARGARG(chain 'HA' and (resid 28 through 220 or (resid 221...HAV310 - 435310 - 435
224CYSCYSALAALA(chain 'HA' and (resid 28 through 220 or (resid 221...HAV451 - 528451 - 528
231ALAALAARGARG(chain 'HB' and (resid 28 through 188 or resid 195...HBW28 - 18728 - 187
232VALVALASNASN(chain 'HB' and (resid 28 through 188 or resid 195...HBW195 - 302195 - 302
233ASNASNARGARG(chain 'HB' and (resid 28 through 188 or resid 195...HBW310 - 435310 - 435
234CYSCYSALAALA(chain 'HB' and (resid 28 through 188 or resid 195...HBW451 - 528451 - 528
241ALAALAARGARG(chain 'HC' and (resid 28 through 188 or resid 195...HCX28 - 18728 - 187
242VALVALASNASN(chain 'HC' and (resid 28 through 188 or resid 195...HCX195 - 302195 - 302
243ASNASNARGARG(chain 'HC' and (resid 28 through 188 or resid 195...HCX310 - 435310 - 435
244CYSCYSALAALA(chain 'HC' and (resid 28 through 188 or resid 195...HCX451 - 528451 - 528
251ALAALAARGARG(chain 'IA' and (resid 28 through 220 or (resid 221...IAY28 - 18728 - 187
252VALVALASNASN(chain 'IA' and (resid 28 through 220 or (resid 221...IAY195 - 302195 - 302
253ASNASNARGARG(chain 'IA' and (resid 28 through 220 or (resid 221...IAY310 - 435310 - 435
254CYSCYSALAALA(chain 'IA' and (resid 28 through 220 or (resid 221...IAY451 - 528451 - 528
261ALAALAARGARG(chain 'IB' and (resid 28 through 188 or resid 195...IBZ28 - 18728 - 187
262VALVALASNASN(chain 'IB' and (resid 28 through 188 or resid 195...IBZ195 - 302195 - 302
263ASNASNARGARG(chain 'IB' and (resid 28 through 188 or resid 195...IBZ310 - 435310 - 435
264CYSCYSALAALA(chain 'IB' and (resid 28 through 188 or resid 195...IBZ451 - 528451 - 528
271ALAALAARGARG(chain 'IC' and (resid 28 through 188 or resid 195...ICAA28 - 18728 - 187
272VALVALASNASN(chain 'IC' and (resid 28 through 188 or resid 195...ICAA195 - 302195 - 302
273ASNASNARGARG(chain 'IC' and (resid 28 through 188 or resid 195...ICAA310 - 435310 - 435
274CYSCYSALAALA(chain 'IC' and (resid 28 through 188 or resid 195...ICAA451 - 528451 - 528
281ALAALAARGARG(chain 'JA' and (resid 28 through 220 or (resid 221...JABA28 - 18728 - 187
282VALVALASNASN(chain 'JA' and (resid 28 through 220 or (resid 221...JABA195 - 302195 - 302
283ASNASNARGARG(chain 'JA' and (resid 28 through 220 or (resid 221...JABA310 - 435310 - 435
284CYSCYSALAALA(chain 'JA' and (resid 28 through 220 or (resid 221...JABA451 - 528451 - 528
291ALAALAARGARG(chain 'JB' and (resid 28 through 188 or resid 195...JBCA28 - 18728 - 187
292VALVALASNASN(chain 'JB' and (resid 28 through 188 or resid 195...JBCA195 - 302195 - 302
293ASNASNARGARG(chain 'JB' and (resid 28 through 188 or resid 195...JBCA310 - 435310 - 435
294CYSCYSALAALA(chain 'JB' and (resid 28 through 188 or resid 195...JBCA451 - 528451 - 528
301ALAALAARGARG(chain 'JC' and (resid 28 through 188 or resid 195...JCDA28 - 18728 - 187
302VALVALASNASN(chain 'JC' and (resid 28 through 188 or resid 195...JCDA195 - 302195 - 302
303ASNASNARGARG(chain 'JC' and (resid 28 through 188 or resid 195...JCDA310 - 435310 - 435
304CYSCYSALAALA(chain 'JC' and (resid 28 through 188 or resid 195...JCDA451 - 528451 - 528
311ALAALAARGARG(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA28 - 18728 - 187
312VALVALASNASN(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA195 - 302195 - 302
313ASNASNARGARG(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA310 - 435310 - 435
314CYSCYSALAALA(chain 'KA' and (resid 28 through 220 or (resid 221...KAEA451 - 528451 - 528
321ALAALAARGARG(chain 'KB' and (resid 28 through 188 or resid 195...KBFA28 - 18728 - 187
322VALVALASNASN(chain 'KB' and (resid 28 through 188 or resid 195...KBFA195 - 302195 - 302
323ASNASNARGARG(chain 'KB' and (resid 28 through 188 or resid 195...KBFA310 - 435310 - 435
324CYSCYSALAALA(chain 'KB' and (resid 28 through 188 or resid 195...KBFA451 - 528451 - 528
331ALAALAARGARG(chain 'KC' and (resid 28 through 188 or resid 195...KCGA28 - 18728 - 187
332VALVALASNASN(chain 'KC' and (resid 28 through 188 or resid 195...KCGA195 - 302195 - 302
333ASNASNARGARG(chain 'KC' and (resid 28 through 188 or resid 195...KCGA310 - 435310 - 435
334CYSCYSALAALA(chain 'KC' and (resid 28 through 188 or resid 195...KCGA451 - 528451 - 528
341ALAALAARGARG(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA28 - 18728 - 187
342VALVALASNASN(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA195 - 302195 - 302
343ASNASNARGARG(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA310 - 435310 - 435
344CYSCYSALAALA(chain 'LA' and (resid 28 through 220 or (resid 221...LAHA451 - 528451 - 528
351ALAALAARGARG(chain 'LB' and (resid 28 through 188 or resid 195...LBIA28 - 18728 - 187
352VALVALASNASN(chain 'LB' and (resid 28 through 188 or resid 195...LBIA195 - 302195 - 302
353ASNASNARGARG(chain 'LB' and (resid 28 through 188 or resid 195...LBIA310 - 435310 - 435
354CYSCYSALAALA(chain 'LB' and (resid 28 through 188 or resid 195...LBIA451 - 528451 - 528
361ALAALAARGARG(chain 'LC' and (resid 28 through 188 or resid 195...LCJA28 - 18728 - 187
362VALVALASNASN(chain 'LC' and (resid 28 through 188 or resid 195...LCJA195 - 302195 - 302
363ASNASNARGARG(chain 'LC' and (resid 28 through 188 or resid 195...LCJA310 - 435310 - 435
364CYSCYSALAALA(chain 'LC' and (resid 28 through 188 or resid 195...LCJA451 - 528451 - 528
371ALAALAARGARG(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA28 - 18728 - 187
372VALVALASNASN(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA195 - 302195 - 302
373ASNASNARGARG(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA310 - 435310 - 435
374CYSCYSALAALA(chain 'MA' and (resid 28 through 220 or (resid 221...MAKA451 - 528451 - 528
381ALAALAARGARG(chain 'MB' and (resid 28 through 188 or resid 195...MBLA28 - 18728 - 187
382VALVALASNASN(chain 'MB' and (resid 28 through 188 or resid 195...MBLA195 - 302195 - 302
383ASNASNARGARG(chain 'MB' and (resid 28 through 188 or resid 195...MBLA310 - 435310 - 435
384CYSCYSALAALA(chain 'MB' and (resid 28 through 188 or resid 195...MBLA451 - 528451 - 528
391ALAALAARGARG(chain 'MC' and (resid 28 through 188 or resid 195...MCMA28 - 18728 - 187
392VALVALASNASN(chain 'MC' and (resid 28 through 188 or resid 195...MCMA195 - 302195 - 302
393ASNASNARGARG(chain 'MC' and (resid 28 through 188 or resid 195...MCMA310 - 435310 - 435
394CYSCYSALAALA(chain 'MC' and (resid 28 through 188 or resid 195...MCMA451 - 528451 - 528
401ALAALAARGARG(chain 'NA' and (resid 28 through 220 or (resid 221...NANA28 - 18728 - 187
402VALVALASNASN(chain 'NA' and (resid 28 through 220 or (resid 221...NANA195 - 302195 - 302
403ASNASNARGARG(chain 'NA' and (resid 28 through 220 or (resid 221...NANA310 - 435310 - 435
404CYSCYSALAALA(chain 'NA' and (resid 28 through 220 or (resid 221...NANA451 - 528451 - 528
411ALAALAARGARG(chain 'NB' and (resid 28 through 188 or resid 195...NBOA28 - 18728 - 187
412VALVALASNASN(chain 'NB' and (resid 28 through 188 or resid 195...NBOA195 - 302195 - 302
413ASNASNARGARG(chain 'NB' and (resid 28 through 188 or resid 195...NBOA310 - 435310 - 435
414CYSCYSALAALA(chain 'NB' and (resid 28 through 188 or resid 195...NBOA451 - 528451 - 528
421ALAALAARGARG(chain 'NC' and (resid 28 through 188 or resid 195...NCPA28 - 18728 - 187
422VALVALASNASN(chain 'NC' and (resid 28 through 188 or resid 195...NCPA195 - 302195 - 302
423ASNASNARGARG(chain 'NC' and (resid 28 through 188 or resid 195...NCPA310 - 435310 - 435
424CYSCYSALAALA(chain 'NC' and (resid 28 through 188 or resid 195...NCPA451 - 528451 - 528
431ALAALAARGARG(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA28 - 18728 - 187
432VALVALASNASN(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA195 - 302195 - 302
433ASNASNARGARG(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA310 - 435310 - 435
434CYSCYSALAALA(chain 'OA' and (resid 28 through 220 or (resid 221...OAQA451 - 528451 - 528
441ALAALAARGARG(chain 'OB' and (resid 28 through 188 or resid 195...OBRA28 - 18728 - 187
442VALVALASNASN(chain 'OB' and (resid 28 through 188 or resid 195...OBRA195 - 302195 - 302
443ASNASNARGARG(chain 'OB' and (resid 28 through 188 or resid 195...OBRA310 - 435310 - 435
444CYSCYSALAALA(chain 'OB' and (resid 28 through 188 or resid 195...OBRA451 - 528451 - 528
451ALAALAARGARG(chain 'OC' and (resid 28 through 188 or resid 195...OCSA28 - 18728 - 187
452VALVALASNASN(chain 'OC' and (resid 28 through 188 or resid 195...OCSA195 - 302195 - 302
453ASNASNARGARG(chain 'OC' and (resid 28 through 188 or resid 195...OCSA310 - 435310 - 435
454CYSCYSALAALA(chain 'OC' and (resid 28 through 188 or resid 195...OCSA451 - 528451 - 528

-
Components

#1: Protein ...
Capsid protein VP1


Mass: 58760.895 Da / Num. of mol.: 45
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/Houston/TCH186/2002/US / Cell line (production host): Sf9
Production host: Insect cell expression vector pTIE1 (others)
References: UniProt: A9YYE4
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 50 / Source method: obtained synthetically / Formula: Cl
#3: Chemical...
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 22 / Source method: obtained synthetically / Formula: Cd / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

-
Experiment

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

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Sample preparation

CrystalDensity Matthews: 4.34 Å3/Da / Density % sol: 71.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.1 M Na Acetate pH 4.6, 0.1 M Cadmium Chloride, 30% PEG 400

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794806 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 29, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794806 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. obs: 841777 / % possible obs: 98.4 % / Redundancy: 3.2 % / Biso Wilson estimate: 67.97 Å2 / Rmerge(I) obs: 0.136 / Rrim(I) all: 0.163 / Net I/σ(I): 7
Reflection shellResolution: 3→3.05 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 1 / Num. unique obs: 38566 / Rpim(I) all: 0.63 / % possible all: 90.5

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1ihm

1ihm


Resolution: 3→30 Å / SU ML: 0.3942 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.4771
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2418 40708 4.97 %
Rwork0.2071 778541 -
obs0.2088 819249 95.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.79 Å2
Refinement stepCycle: LAST / Resolution: 3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms176443 0 76 3 176522
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036181805
X-RAY DIFFRACTIONf_angle_d0.7703249531
X-RAY DIFFRACTIONf_chiral_restr0.051927916
X-RAY DIFFRACTIONf_plane_restr0.006433286
X-RAY DIFFRACTIONf_dihedral_angle_d3.8767107203
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.030.37368890.331217333X-RAY DIFFRACTION64.19
3.03-3.070.362710150.313319647X-RAY DIFFRACTION72.73
3.07-3.110.353310760.296321566X-RAY DIFFRACTION79.91
3.11-3.150.328511420.291922952X-RAY DIFFRACTION84.83
3.15-3.190.338812750.286624172X-RAY DIFFRACTION89.47
3.19-3.230.326612920.282725171X-RAY DIFFRACTION93.12
3.23-3.280.319813190.28825893X-RAY DIFFRACTION96.03
3.28-3.330.332213760.268626339X-RAY DIFFRACTION97.66
3.33-3.380.311913690.2726660X-RAY DIFFRACTION98.54
3.38-3.430.304814110.260526759X-RAY DIFFRACTION98.98
3.43-3.490.291314400.255126803X-RAY DIFFRACTION99.31
3.49-3.560.303414340.25926849X-RAY DIFFRACTION99.5
3.56-3.620.278613820.234826993X-RAY DIFFRACTION99.67
3.62-3.70.275913700.236827003X-RAY DIFFRACTION99.84
3.7-3.780.273714020.225926944X-RAY DIFFRACTION99.89
3.78-3.870.265814950.226526975X-RAY DIFFRACTION99.94
3.87-3.960.249514530.207527068X-RAY DIFFRACTION99.94
3.96-4.070.236413690.208227040X-RAY DIFFRACTION99.95
4.07-4.190.232414310.193727020X-RAY DIFFRACTION99.92
4.19-4.320.215214250.17727113X-RAY DIFFRACTION99.92
4.32-4.480.20713140.17327150X-RAY DIFFRACTION99.89
4.48-4.660.197913500.164827109X-RAY DIFFRACTION99.9
4.66-4.870.186413820.158527189X-RAY DIFFRACTION99.95
4.87-5.120.196414830.163727094X-RAY DIFFRACTION99.98
5.12-5.440.20814840.171327082X-RAY DIFFRACTION99.99
5.44-5.860.224213740.184227251X-RAY DIFFRACTION99.99
5.86-6.450.232614860.197127197X-RAY DIFFRACTION99.97
6.45-7.370.212413910.186627330X-RAY DIFFRACTION99.82
7.37-9.230.195614960.163727352X-RAY DIFFRACTION99.99
9.23-300.2115830.200127487X-RAY DIFFRACTION99.06

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