Pawel A. Penczek, Ph.D

Professor and Co-Director
Structural Biology Imaging Center

Description of Research


We are interested in the determination of three-dimensional structures of large macromolecular complexes with low or non-existing symmetry in single-particle form using stain and cryo-electron microscopy (cryo-EM), and computer image processing techniques.

Our main area of interest is high-resolution cryo-EM and the development of efficient and largely automatic tools for single particle analysis and three-dimensional reconstruction. Due to a very low Signal-To-Noise Ratio of EM data, there is a necessity to collect and merge large numbers (in excess of 100,000) of individual particle images. We develop, in collaboration with other groups, a single particle software package SPARX (Hohn, et al). SPARX is provided free of charge as a service to the scientific community and its main features include:

  1. New generation of 2D and 3D alignment protocols.
  2. Ab initio structure determination programs.
  3. Resampling methods for investigation of structural heterogeneity (3D variance).
  4. Advanced code for multivariate statistical analysis (PCA, Varimax),
  5. New generation of interpolation methods relaxing the need for oversampling the data.
  6. Wiki-based interactive documentation
  7. Extensive C++ library of general and EM-specific image operations with Python bindings, thus accessible to Python programmer.
  8. All structure determination applications written as user transparent Python scripts
  9. All major scripts parallelized for clusters of workstations using MPI.

Sparx is available for download at

Unconstrained by crystal packing, the molecule in a single particle specimen can be thought to exhibit the entire range of native conformations. The ability to find the structure of each conformer is one of the most important potential assets of 3D cryo-EM of single particles. On the other hand, the realization of high resolution for each of these conformers poses daunting problems of data collection and processing, considering the statistical requirements stated before. Therefore, we are also interested in the development of efficient and robust computational methods of structure refinement and structure validation in the presence of multiple conformational or binding states.

faculty-pawel-penczek-2006imageOne area of focus is determination of the structure of a newly identified protein called HRS (hepatocyte growth factor regulated tyrosine kinase substrate) (Pullan et al., Structure, 2006). HRS is phosphorylated by various kinases in response to a variety of growth factors and is expressed in the cytoplasm of all cells. In addition, HRS was also implicated in exocytosis of synaptic vesicles. The main interest is in its regulatory functions. The determination by cryo-EM of the tertiary structure of HRS to 16Å together with knowledge of its amino acid sequence has enabled us to propose a model of hexameric HRS insertion into the endosomal membrane. With the knowledge of the native structure, we will continue the structural determination of HRS complexes, including HRS bound to ubiquitinated cargo and other known binding proteins involved in the process of cargo sorting and vesicular trafficking.

The structure is hexameric with six subunits arranged in an anti-parallel fashion. The background shows a cryo micrograph with side and end views of single particles of HRS from which the structure was computed.

Contact Information

UTHealth Medical School
Department of Biochemistry and Molecular Biology
6431 Fannin Street, MSB 6. 220
Houston, Texas 77030

713-500-5416  Direct  713-500-0652 Fax


Ph.D. - Warsaw University

Postdoctoral Fellow - Wadsworth Center, Albany NY

Research Interests

Cryo-electron microscopy, Single particle reconstruction


Iterative stable alignment and clustering of 2D transmission electron microscope images.

Yang Z, Fang J, Chittuluru J, Asturias FJ, Penczek PA.

Structure. 2012 Feb 8;20(2):237-47. doi: 10.1016/j.str.2011.12.007.

PMID: 22325773

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CTER-rapid estimation of CTF parameters with error assessment

Penczek PA, Fang J, Li X, Cheng Y, Loerke J, Spahn CM

Ultramicroscopy. 2014 May;140:9-19. doi: 10.1016/j.ultramic.2014.01.009. Epub 2014 Feb 7.

PMCID:  PMC4016771

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Molecular Imprinting as a Signal-Activation Mechanism of the Viral RNA Sensor RIG-I

Wu B, Peisley A, Tetrault D, Li Z, Egelman EH, Magor KE, Walz T, Penczek PA, Hur S.

Mol Cell. 2014 Aug 21;55(4):511-23. doi: 10.1016/j.molcel.2014.06.010. Epub 2014 Jul 10.


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Visualization of arrestin recruitment by a G-protein-coupled receptor

Shukla AK, Westfield GH, Xiao K, Reis RI, Huang LY, Tripathi-Shukla P, Qian J, Li S, Blanc A, Oleskie AN, Dosey AM, Su M, Liang CR, Gu LL, Shan JM, Chen X, Hanna R, Choi M, Yao XJ, Klink BU, Kahsai AW, Sidhu SS, Koide S, Penczek PA, Kossiakoff AA, Woods VL Jr, Kobilka BK, Skiniotis G, Lefkowitz RJ.

Nature. 2014 Aug 14;512(7513):218-22

PMCID:  PMC4134437

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