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SCHEDULE 13D/A 0000902664-21-004741 0001410830 XXXXXXXX LIVE 3 Common Stock, par value $0.00001 per share 05/16/2025 false 0001501796 05153U107 Aura Biosciences, Inc. 80 GUEST STREET BOSTON MA 02135 Joseph Downing 603-956-9145 Matrix Capital Management Company LP 1000 Winter Street, Suite 4500 Waltham MA 02451 Ele Klein & Adriana Schwartz 212-756-2000 Schulte Roth & Zabel LLP 919 Third Avenue New York NY 10022 0001410830 N Matrix Capital Management Company LP OO N DE 0.00 6922870.00 0.00 6922870.00 6922870.00 N 11.17 IA PN 0001548144 N David E. Goel OO N X1 0.00 6922870.00 0.00 6922870.00 6922870.00 N 11.17 IN HC Common Stock, par value $0.00001 per share Aura Biosciences, Inc. 80 GUEST STREET BOSTON MA 02135 The following constitutes Amendment No. 3 to the Schedule 13D filed by the undersigned (the "Amendment No. 3"). This Amendment No. 3 amends and restates Item 5(a) and supplements Items 6 and 7, as set forth below. See rows (11) and (13) of the cover pages to this Schedule 13D for the aggregate number of Common Stock and percentages of the Common Stock beneficially owned by each Reporting Person. The percentages used in this Schedule 13D as of the date hereof are calculated based upon 61,960,877 shares of Common Stock outstanding, as disclosed in the Issuer's prospectus supplement filed pursuant to Rule 424(b)(5) with the SEC on May 16, 2025, after giving effect to the completion of the offering, as described therein (the "2025 Offering"). In connection with the 2025 Offering, on May 16, 2025, the Matrix Fund entered into a lock-up agreement with the underwriters of the 2025 Offering that restrict its ability to sell or transfer its shares of Common Stock or any securities convertible into or exercisable or exchangeable for shares of Common Stock until the 90th day after the date of the Underwriting Agreement entered into by the Issuer in connection with the 2025 Offering without the prior written consent of the representatives of the underwriters that participated in the 2025 Offering, subject to certain exceptions (the "2025 Offering Lock-Up Agreement"). The foregoing description of the 2025 Offering Lock-Up Agreement does not purport to be complete and is qualified in its entirety by reference to the full text of the 2025 Offering Lock-Up Agreement which is attached hereto as Exhibit F and is incorporated herein by reference. Exhibit F: Form of the 2025 Offering Lock-Up Agreement (incorporated herein by reference to Exhibit I to Exhibit 1.1 to the Issuer's Current Report on Form 8-K filed with the SEC on May 16, 2025). Matrix Capital Management Company LP /s/ David E. Goel David E. Goel, Managing General Partner 05/19/2025 David E. Goel /s/ David E. Goel David E. Goel, Individually 05/19/2025