5UP4 | pdb_00005up4

Structure of the HIV-1 Capsid Protein and spacer peptide 1 by Cryo-EM

• PDB DOI: https://doi.org/10.2210/pdb5UP4/pdb
• EM Map EMD-8582: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-02-01 Released: 2017-12-06 
• Deposition Author(s): Perilla, J.R., Schirra, R., Zhang, P., Schulten, K.
• Funding Organization(s): National Institutes of Health

---

Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 9.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

Starting Models: experimental

Literature

Quenching protein dynamics interferes with HIV capsid maturation.

Wang, M., Quinn, C.M., Perilla, J.R., Zhang, H., Shirra, R., Hou, G., Byeon, I.J., Suiter, C.L., Ablan, S., Urano, E., Nitz, T.J., Aiken, C., Freed, E.O., Zhang, P., Schulten, K., Gronenborn, A.M., Polenova, T.

(2017) Nat Commun 8: 1779-1779

• PubMed: 29176596 
• DOI: https://doi.org/10.1038/s41467-017-01856-y
• Primary Citation Related Structures: 
  5UP4


• PubMed Abstract: 
  

  Maturation of HIV-1 particles encompasses a complex morphological transformation of Gag via an orchestrated series of proteolytic cleavage events. A longstanding question concerns the structure of the C-terminal region of CA and the peptide SP1 (CA-SP1), which represents an intermediate during maturation of the HIV-1 virus. By integrating NMR, cryo-EM, and molecular dynamics simulations, we show that in CA-SP1 tubes assembled in vitro, which represent the features of an intermediate assembly state during maturation, the SP1 peptide exists in a dynamic helix-coil equilibrium, and that the addition of the maturation inhibitors Bevirimat and DFH-055 causes stabilization of a helical form of SP1. Moreover, the maturation-arresting SP1 mutation T8I also induces helical structure in SP1 and further global dynamical and conformational changes in CA. Overall, our results show that dynamics of CA and SP1 are critical for orderly HIV-1 maturation and that small molecules can inhibit maturation by perturbing molecular motions.

---

Organizational Affiliation: 
• Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA.
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA. [e-mail].
University of Illinois, Theoretical and Computational Biophysics Group, Urbana, IL, 61801, USA. [e-mail].
Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA.
HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
DFH Pharma, Gaithersburg, MD, 20886, USA.
Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA.
Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, OX3 7BN, UK.
University of Illinois, Theoretical and Computational Biophysics Group, Urbana, IL, 61801, USA.
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA. [e-mail].
Department of Structural Biology, University of Pittsburgh School of Medicine, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA. [e-mail].
Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, 19716, USA. [e-mail].
Pittsburgh Center for HIV Protein Interactions, University of Pittsburgh School of Medicine, 1051 Biomedical Science Tower 3, 3501 Fifth Ave., Pittsburgh, PA, 15261, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 18-mer - A18 

Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 Local Symmetry: Cyclic - C6  (Explore in 3D)
Local Stoichiometry: Homo 6-mer - A6 

Biological assembly 1 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 443.78 kDa 
• Atom Count: 31,068 
• Modeled Residue Count: 3,978 
• Deposited Residue Count: 3,978 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Capsid Protein and spacer peptide 1	A [auth B], B [auth K], C [auth L], D [auth M], E [auth N], F [auth O], G [auth P], H [auth Q], I [auth R], J [auth S], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H], Q [auth I], R [auth J]	221	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: gag
UniProt
Find proteins for B6DRA0 (Human immunodeficiency virus type 1) Explore B6DRA0  Go to UniProtKB:  B6DRA0

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 9.00 Å
• Aggregation State: HELICAL ARRAY 
• Reconstruction Method: HELICAL 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	FREALIGN

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2017-12-06 
Deposition Author(s): Perilla, J.R., Schirra, R., Zhang, P., Schulten, K.

---

Funding Organization	Location	Grant Number
National Institutes of Health	United States	P50 GM082251

Revision History  

• Version 1.0: 2017-12-06
  Type: Initial release
  
• Version 1.1: 2017-12-13
  Changes: Refinement description
• Version 1.2: 2024-11-20
  Changes: Data collection, Database references, Refinement description, Structure summary