7K6V | pdb_00007k6v

Crystal Structure of Virus-like Particles of GII.4 Norovirus Houston virus (HOV)

PDB DOI: https://doi.org/10.2210/pdb7K6V/pdb

Classification: VIRUS LIKE PARTICLE
Organism(s): Norovirus Hu/Houston/TCH186/2002/US
Expression System: Insect cell expression vector pTIE1
Mutation(s): No

Deposited: 2020-09-21 Released: 2022-03-02
Deposition Author(s): Hu, L., Prasad, B.V.V.
Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.242 (Depositor), 0.242 (DCC)
R-Value Work:
0.207 (Depositor), 0.207 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Crystal structure of GII.4 Norovirus capsid reveals inherent conformational flexibility of the capsid protein

Hu, L., Prasad, B.V.V.

To be published.

Macromolecule Content

Total Structure Weight: 2,648.55 kDa
Atom Count: 176,522
Modeled Residue Count: 22,902
Deposited Residue Count: 24,300
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Capsid protein VP1	A [auth AA] AA [auth IC] B [auth AB] BA [auth JA] C [auth AC] A [auth AA], AA [auth IC], B [auth AB], BA [auth JA], C [auth AC], CA [auth JB], D [auth BA], DA [auth JC], E [auth BB], EA [auth KA], F [auth BC], FA [auth KB], G [auth CA], GA [auth KC], H [auth CB], HA [auth LA], I [auth CC], IA [auth LB], J [auth DA], JA [auth LC], K [auth DB], KA [auth MA], L [auth DC], LA [auth MB], M [auth EA], MA [auth MC], N [auth EB], NA, O [auth EC], OA [auth NB], P [auth FA], PA [auth NC], Q [auth FB], QA [auth OA], R [auth FC], RA [auth OB], S [auth GA], SA [auth OC], T [auth GB], U [auth GC], V [auth HA], W [auth HB], X [auth HC], Y [auth IA], Z [auth IB]	540	Norovirus Hu/Houston/TCH186/2002/US	Mutation(s): 0
UniProt
Find proteins for A9YYE4 (Norovirus Hu/Houston/TCH186/2002/US) Explore A9YYE4 Go to UniProtKB: A9YYE4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A9YYE4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CD (Subject of Investigation/LOI) Query on CD Download:Ideal Coordinates CCD File SDF format, chain ZB [auth GA] SDF format, chain ZA [auth BA] SDF format, chain YB [auth FC] SDF format, chain XA [auth AC] SDF format, chain VB [auth FA] SDF format, chain UC [auth KB] SDF format, chain UB [auth EC] SDF format, chain TB [auth EB] SDF format, chain RC [auth KA] SDF format, chain QC [auth JC] SDF format, chain PB [auth EA] SDF format, chain MC [auth JA] SDF format, chain LD [auth OA] SDF format, chain KB [auth DA] SDF format, chain JD [auth NC] SDF format, chain HC [auth IA] SDF format, chain FC [auth HC] SDF format, chain ED [auth MB] SDF format, chain EB [auth CA] SDF format, chain CB [auth BC] SDF format, chain BC [auth GB] SDF format, chain AD [auth MA] MOL2 format, chain ZB [auth GA] MOL2 format, chain ZA [auth BA] MOL2 format, chain YB [auth FC] MOL2 format, chain XA [auth AC] MOL2 format, chain VB [auth FA] MOL2 format, chain UC [auth KB] MOL2 format, chain UB [auth EC] MOL2 format, chain TB [auth EB] MOL2 format, chain RC [auth KA] MOL2 format, chain QC [auth JC] MOL2 format, chain PB [auth EA] MOL2 format, chain MC [auth JA] MOL2 format, chain LD [auth OA] MOL2 format, chain KB [auth DA] MOL2 format, chain JD [auth NC] MOL2 format, chain HC [auth IA] MOL2 format, chain FC [auth HC] MOL2 format, chain ED [auth MB] MOL2 format, chain EB [auth CA] MOL2 format, chain CB [auth BC] MOL2 format, chain BC [auth GB] MOL2 format, chain AD [auth MA] mmCIF format, chain ZB [auth GA] mmCIF format, chain ZA [auth BA] mmCIF format, chain YB [auth FC] mmCIF format, chain XA [auth AC] mmCIF format, chain VB [auth FA] mmCIF format, chain UC [auth KB] mmCIF format, chain UB [auth EC] mmCIF format, chain TB [auth EB] mmCIF format, chain RC [auth KA] mmCIF format, chain QC [auth JC] mmCIF format, chain PB [auth EA] mmCIF format, chain MC [auth JA] mmCIF format, chain LD [auth OA] mmCIF format, chain KB [auth DA] mmCIF format, chain JD [auth NC] mmCIF format, chain HC [auth IA] mmCIF format, chain FC [auth HC] mmCIF format, chain ED [auth MB] mmCIF format, chain EB [auth CA] mmCIF format, chain CB [auth BC] mmCIF format, chain BC [auth GB] mmCIF format, chain AD [auth MA]	AD [auth MA] BC [auth GB] CB [auth BC] EB [auth CA] ED [auth MB] AD [auth MA], BC [auth GB], CB [auth BC], EB [auth CA], ED [auth MB], FC [auth HC], HC [auth IA], JD [auth NC], KB [auth DA], LD [auth OA], MC [auth JA], PB [auth EA], QC [auth JC], RC [auth KA], TB [auth EB], UB [auth EC], UC [auth KB], VB [auth FA], XA [auth AC], YB [auth FC], ZA [auth BA], ZB [auth GA]	CADMIUM ION Cd WLZRMCYVCSSEQC-UHFFFAOYSA-N		Interactions Focus chain AD [auth MA] Focus chain BC [auth GB] Focus chain CB [auth BC] Focus chain EB [auth CA] Focus chain ED [auth MB] Focus chain FC [auth HC] Focus chain HC [auth IA] Focus chain JD [auth NC] Focus chain KB [auth DA] Focus chain LD [auth OA] Focus chain MC [auth JA] Focus chain PB [auth EA] Focus chain QC [auth JC] Focus chain RC [auth KA] Focus chain TB [auth EB] Focus chain UB [auth EC] Focus chain UC [auth KB] Focus chain VB [auth FA] Focus chain XA [auth AC] Focus chain YB [auth FC] Focus chain ZA [auth BA] Focus chain ZB [auth GA] Interactions & Density Focus chain AD [auth MA] Focus chain BC [auth GB] Focus chain CB [auth BC] Focus chain EB [auth CA] Focus chain ED [auth MB] Focus chain FC [auth HC] Focus chain HC [auth IA] Focus chain JD [auth NC] Focus chain KB [auth DA] Focus chain LD [auth OA] Focus chain MC [auth JA] Focus chain PB [auth EA] Focus chain QC [auth JC] Focus chain RC [auth KA] Focus chain TB [auth EB] Focus chain UB [auth EC] Focus chain UC [auth KB] Focus chain VB [auth FA] Focus chain XA [auth AC] Focus chain YB [auth FC] Focus chain ZA [auth BA] Focus chain ZB [auth GA]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain LC [auth JA] MOL2 format, chain LC [auth JA] mmCIF format, chain LC [auth JA]	LC [auth JA]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain LC [auth JA] Interactions & Density Focus chain LC [auth JA]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain ZC [auth LC] SDF format, chain YC [auth LC] SDF format, chain YA [auth AC] SDF format, chain XC [auth LA] SDF format, chain XB [auth FA] SDF format, chain WC [auth KC] SDF format, chain WB [auth FA] SDF format, chain WA [auth AB] SDF format, chain VC [auth KC] SDF format, chain VA [auth AA] SDF format, chain UA [auth AA] SDF format, chain TC [auth KA] SDF format, chain TA [auth AA] SDF format, chain SC [auth KA] SDF format, chain SB [auth EA] SDF format, chain RB [auth EA] SDF format, chain QB [auth EA] SDF format, chain PC [auth JA] SDF format, chain OC [auth JA] SDF format, chain OB [auth DC] SDF format, chain ND [auth OA] SDF format, chain NC [auth JA] SDF format, chain NB [auth DC] SDF format, chain MD [auth OA] SDF format, chain MB [auth DB] SDF format, chain LB [auth DA] SDF format, chain KD [auth NC] SDF format, chain KC [auth IA] SDF format, chain JC [auth IA] SDF format, chain JB [auth CC] SDF format, chain ID [auth NA] SDF format, chain IC [auth IA] SDF format, chain IB [auth CC] SDF format, chain HD [auth NA] SDF format, chain HB [auth CC] SDF format, chain GD [auth MC] SDF format, chain GC [auth HC] SDF format, chain GB [auth CA] SDF format, chain FD [auth MC] SDF format, chain FB [auth CA] SDF format, chain EC [auth HA] SDF format, chain DD [auth MA] SDF format, chain DC [auth GC] SDF format, chain DB [auth BC] SDF format, chain CD [auth MA] SDF format, chain CC [auth GC] SDF format, chain BD [auth MA] SDF format, chain BB [auth BA] SDF format, chain AC [auth GA] SDF format, chain AB [auth BA] MOL2 format, chain ZC [auth LC] MOL2 format, chain YC [auth LC] MOL2 format, chain YA [auth AC] MOL2 format, chain XC [auth LA] MOL2 format, chain XB [auth FA] MOL2 format, chain WC [auth KC] MOL2 format, chain WB [auth FA] MOL2 format, chain WA [auth AB] MOL2 format, chain VC [auth KC] MOL2 format, chain VA [auth AA] MOL2 format, chain UA [auth AA] MOL2 format, chain TC [auth KA] MOL2 format, chain TA [auth AA] MOL2 format, chain SC [auth KA] MOL2 format, chain SB [auth EA] MOL2 format, chain RB [auth EA] MOL2 format, chain QB [auth EA] MOL2 format, chain PC [auth JA] MOL2 format, chain OC [auth JA] MOL2 format, chain OB [auth DC] MOL2 format, chain ND [auth OA] MOL2 format, chain NC [auth JA] MOL2 format, chain NB [auth DC] MOL2 format, chain MD [auth OA] MOL2 format, chain MB [auth DB] MOL2 format, chain LB [auth DA] MOL2 format, chain KD [auth NC] MOL2 format, chain KC [auth IA] MOL2 format, chain JC [auth IA] MOL2 format, chain JB [auth CC] MOL2 format, chain ID [auth NA] MOL2 format, chain IC [auth IA] MOL2 format, chain IB [auth CC] MOL2 format, chain HD [auth NA] MOL2 format, chain HB [auth CC] MOL2 format, chain GD [auth MC] MOL2 format, chain GC [auth HC] MOL2 format, chain GB [auth CA] MOL2 format, chain FD [auth MC] MOL2 format, chain FB [auth CA] MOL2 format, chain EC [auth HA] MOL2 format, chain DD [auth MA] MOL2 format, chain DC [auth GC] MOL2 format, chain DB [auth BC] MOL2 format, chain CD [auth MA] MOL2 format, chain CC [auth GC] MOL2 format, chain BD [auth MA] MOL2 format, chain BB [auth BA] MOL2 format, chain AC [auth GA] MOL2 format, chain AB [auth BA] mmCIF format, chain ZC [auth LC] mmCIF format, chain YC [auth LC] mmCIF format, chain YA [auth AC] mmCIF format, chain XC [auth LA] mmCIF format, chain XB [auth FA] mmCIF format, chain WC [auth KC] mmCIF format, chain WB [auth FA] mmCIF format, chain WA [auth AB] mmCIF format, chain VC [auth KC] mmCIF format, chain VA [auth AA] mmCIF format, chain UA [auth AA] mmCIF format, chain TC [auth KA] mmCIF format, chain TA [auth AA] mmCIF format, chain SC [auth KA] mmCIF format, chain SB [auth EA] mmCIF format, chain RB [auth EA] mmCIF format, chain QB [auth EA] mmCIF format, chain PC [auth JA] mmCIF format, chain OC [auth JA] mmCIF format, chain OB [auth DC] mmCIF format, chain ND [auth OA] mmCIF format, chain NC [auth JA] mmCIF format, chain NB [auth DC] mmCIF format, chain MD [auth OA] mmCIF format, chain MB [auth DB] mmCIF format, chain LB [auth DA] mmCIF format, chain KD [auth NC] mmCIF format, chain KC [auth IA] mmCIF format, chain JC [auth IA] mmCIF format, chain JB [auth CC] mmCIF format, chain ID [auth NA] mmCIF format, chain IC [auth IA] mmCIF format, chain IB [auth CC] mmCIF format, chain HD [auth NA] mmCIF format, chain HB [auth CC] mmCIF format, chain GD [auth MC] mmCIF format, chain GC [auth HC] mmCIF format, chain GB [auth CA] mmCIF format, chain FD [auth MC] mmCIF format, chain FB [auth CA] mmCIF format, chain EC [auth HA] mmCIF format, chain DD [auth MA] mmCIF format, chain DC [auth GC] mmCIF format, chain DB [auth BC] mmCIF format, chain CD [auth MA] mmCIF format, chain CC [auth GC] mmCIF format, chain BD [auth MA] mmCIF format, chain BB [auth BA] mmCIF format, chain AC [auth GA] mmCIF format, chain AB [auth BA]	AB [auth BA] AC [auth GA] BB [auth BA] BD [auth MA] CC [auth GC] AB [auth BA], AC [auth GA], BB [auth BA], BD [auth MA], CC [auth GC], CD [auth MA], DB [auth BC], DC [auth GC], DD [auth MA], EC [auth HA], FB [auth CA], FD [auth MC], GB [auth CA], GC [auth HC], GD [auth MC], HB [auth CC], HD [auth NA], IB [auth CC], IC [auth IA], ID [auth NA], JB [auth CC], JC [auth IA], KC [auth IA], KD [auth NC], LB [auth DA], MB [auth DB], MD [auth OA], NB [auth DC], NC [auth JA], ND [auth OA], OB [auth DC], OC [auth JA], PC [auth JA], QB [auth EA], RB [auth EA], SB [auth EA], SC [auth KA], TA [auth AA], TC [auth KA], UA [auth AA], VA [auth AA], VC [auth KC], WA [auth AB], WB [auth FA], WC [auth KC], XB [auth FA], XC [auth LA], YA [auth AC], YC [auth LC], ZC [auth LC]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AB [auth BA] Focus chain AC [auth GA] Focus chain BB [auth BA] Focus chain BD [auth MA] Focus chain CC [auth GC] Focus chain CD [auth MA] Focus chain DB [auth BC] Focus chain DC [auth GC] Focus chain DD [auth MA] Focus chain EC [auth HA] Focus chain FB [auth CA] Focus chain FD [auth MC] Focus chain GB [auth CA] Focus chain GC [auth HC] Focus chain GD [auth MC] Focus chain HB [auth CC] Focus chain HD [auth NA] Focus chain IB [auth CC] Focus chain IC [auth IA] Focus chain ID [auth NA] Focus chain JB [auth CC] Focus chain JC [auth IA] Focus chain KC [auth IA] Focus chain KD [auth NC] Focus chain LB [auth DA] Focus chain MB [auth DB] Focus chain MD [auth OA] Focus chain NB [auth DC] Focus chain NC [auth JA] Focus chain ND [auth OA] Focus chain OB [auth DC] Focus chain OC [auth JA] Focus chain PC [auth JA] Focus chain QB [auth EA] Focus chain RB [auth EA] Focus chain SB [auth EA] Focus chain SC [auth KA] Focus chain TA [auth AA] Focus chain TC [auth KA] Focus chain UA [auth AA] Focus chain VA [auth AA] Focus chain VC [auth KC] Focus chain WA [auth AB] Focus chain WB [auth FA] Focus chain WC [auth KC] Focus chain XB [auth FA] Focus chain XC [auth LA] Focus chain YA [auth AC] Focus chain YC [auth LC] Focus chain ZC [auth LC] Interactions & Density Focus chain AB [auth BA] Focus chain AC [auth GA] Focus chain BB [auth BA] Focus chain BD [auth MA] Focus chain CC [auth GC] Focus chain CD [auth MA] Focus chain DB [auth BC] Focus chain DC [auth GC] Focus chain DD [auth MA] Focus chain EC [auth HA] Focus chain FB [auth CA] Focus chain FD [auth MC] Focus chain GB [auth CA] Focus chain GC [auth HC] Focus chain GD [auth MC] Focus chain HB [auth CC] Focus chain HD [auth NA] Focus chain IB [auth CC] Focus chain IC [auth IA] Focus chain ID [auth NA] Focus chain JB [auth CC] Focus chain JC [auth IA] Focus chain KC [auth IA] Focus chain KD [auth NC] Focus chain LB [auth DA] Focus chain MB [auth DB] Focus chain MD [auth OA] Focus chain NB [auth DC] Focus chain NC [auth JA] Focus chain ND [auth OA] Focus chain OB [auth DC] Focus chain OC [auth JA] Focus chain PC [auth JA] Focus chain QB [auth EA] Focus chain RB [auth EA] Focus chain SB [auth EA] Focus chain SC [auth KA] Focus chain TA [auth AA] Focus chain TC [auth KA] Focus chain UA [auth AA] Focus chain VA [auth AA] Focus chain VC [auth KC] Focus chain WA [auth AB] Focus chain WB [auth FA] Focus chain WC [auth KC] Focus chain XB [auth FA] Focus chain XC [auth LA] Focus chain YA [auth AC] Focus chain YC [auth LC] Focus chain ZC [auth LC]