Determining the architectures of macromolecular assemblies

ABSTRACT To understand the workings of a living cell, we need to know the architectures of its macromolecular assemblies. Here we show how proteomic data can be used to determine such

structures. The process involves the collection of sufficient and diverse high-quality data, translation of these data into spatial restraints, and an optimization that uses the restraints

to generate an ensemble of structures consistent with the data. Analysis of the ensemble produces a detailed architectural map of the assembly. We developed our approach on a challenging

model system, the nuclear pore complex (NPC). The NPC acts as a dynamic barrier, controlling access to and from the nucleus, and in yeast is a 50 MDa assembly of 456 proteins. The resulting

structure, presented in an accompanying paper, reveals the configuration of the proteins in the NPC, providing insights into its evolution and architectural principles. The present approach

should be applicable to many other macromolecular assemblies. Access through your institution Buy or subscribe This is a preview of subscription content, access via your institution ACCESS

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Article 29 November 2021 A MULTI-SCALE MAP OF CELL STRUCTURE FUSING PROTEIN IMAGES AND INTERACTIONS Article 24 November 2021 A QUANTITATIVE MAP OF NUCLEAR PORE ASSEMBLY REVEALS TWO DISTINCT

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Scholar  Download references ACKNOWLEDGEMENTS We thank H. Shio for performing the electron microscopic studies; J. Fanghänel, M. Niepel and C. Strambio-de-Castillia for help in developing

the affinity purification techniques; M. Magnasco for discussions and advice; A. Kruchinsky for assistance with mass spectrometry; M. Topf, D. Korkin, F. Davis, M.-Y. Shen, F. Foerster, N.

Eswar, M. Kim, D. Russel, B. Peterson and B. Webb for many discussions about structure characterization by satisfaction of spatial restraints; C. Johnson, S. G. Parker and C. Silva, T.

Ferrin and T. Goddard for preparation of some figures; and S. Pulapura and X. J. Zhou for their help with the design of the conditional diameter restraint. We are grateful to J. Aitchison

for discussion and insightful suggestions. We also thank all other members of the Chait, Rout and Sali laboratories for their assistance. We acknowledge support from an Irma T. Hirschl

Career Scientist Award (M.P.R.), a Sinsheimer Scholar Award (M.P.R.), a grant from the Rita Allen Foundation (M.P.R.), a grant from the American Cancer Society (M.P.R.), the Sandler Family

Supporting Foundation (A.S.), the Human Frontier Science Program (A.S., L.M.V.), NSF (A.S.), and grants from the National Institutes of Health (B.T.C., M.P.R., A.S.), as well as computer

hardware gifts from R. Conway, M. Homer, Intel, Hewlett-Packard, IBM and Netapp (A.S.). AUTHOR INFORMATION Author notes * Svetlana Dokudovskaya, Liesbeth M. Veenhoff, Julia Kipper, Damien

Devos, Adisetyantari Suprapto & Orit Karni-Schmidt Present address: Present addresses: Laboratory of Nucleocytoplasmic Transport, Institut Jacques Monod, 2 place Jussieu, Tour 43, Paris

75251, France (S.D.); Department of Biochemistry, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands (L.M.V.); German Aerospace Center (PT-DLR), Heinrich-Konen-Strasse

1, D-53227 Bonn, Germany (J.K.); Structural Bioinformatics, EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany (D.D.); Office of Technology Transfer, The Rockefeller University, 1230 York

Avenue, New York, New York 10065, USA (A.S.); Herbert Irving Comprehensive Cancer Center, Columbia University, 1130 St Nicholas Avenue, New York, New York 10032, USA (O.K.-S.)., New York *

Frank Alber, Svetlana Dokudovskaya and Liesbeth M. Veenhoff: These authors contributed equally to this work. AUTHORS AND AFFILIATIONS * Department of Bioengineering and Therapeutic Sciences,

Department of Pharmaceutical Chemistry, and California Institute for Quantitative Biosciences, Byers Hall, Suite 503B, 1700 4th Street, University of California at San Francisco, San

Francisco, California 94158-2330, USA, California Frank Alber, Damien Devos & Andrej Sali * Laboratory of Cellular and Structural Biology, and,, California Svetlana Dokudovskaya, 

Liesbeth M. Veenhoff, Julia Kipper, Adisetyantari Suprapto, Orit Karni-Schmidt, Rosemary Williams & Michael P. Rout * Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The

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also search for this author inPubMed Google Scholar CORRESPONDING AUTHORS Correspondence to Brian T. Chait, Michael P. Rout or Andrej Sali. SUPPLEMENTARY INFORMATION SUPPLEMENTARY

INFORMATION The file contains Supplementary Methods, Supplementary Figures 1-27, Supplementary Tables 1-10 and additional references. (PDF 8230 kb) RIGHTS AND PERMISSIONS Reprints and

permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Alber, F., Dokudovskaya, S., Veenhoff, L. _et al._ Determining the architectures of macromolecular assemblies. _Nature_ 450, 683–694 (2007).

https://doi.org/10.1038/nature06404 Download citation * Received: 30 August 2007 * Accepted: 22 October 2007 * Published: 29 November 2007 * Issue Date: 29 November 2007 * DOI:

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