Sec Form 4 Filing - Flagship Ventures Fund IV General Partner LLC @ Rubius Therapeutics, Inc. - 2021-03-19

FORM 4 Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).

UNITED STATES SECURITIES AND EXCHANGE COMMISSION Washington, D.C. 20549 STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940

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1. Name and Address of Reporting Person Flagship Ventures Fund IV General Partner LLC 2. Issuer Name and Ticker or Trading Symbol Rubius Therapeutics, Inc. [ RUBY] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) _____ Director X __ 10% Owner _____ Officer (give title below) _____ Other (specify below) (Last) (First) (Middle) 55 CAMBRIDGE PARKWAY, SUITE 800E 3. Date of Earliest Transaction (MM/DD/YY) 03/19/2021 (Street) CAMBRIDGE, MA02142 4. If Amendment, Date Original Filed (MM/DD/YY) 6. Individual or Joint/Group Filing (Check Applicable Line) _____ Form filed by One Reporting Person __ X __ Form filed by More than One Reporting Person (City) (State) (Zip)

Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned 1.Title of Security (Instr. 3) 2. Transaction Date (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 3. Transaction Code (Instr. 8) 4. Securities Acquired (A) or Disposed of (D) (Instr. 3, 4 and 5) 5. Amount of Securities Beneficially Owned Following Reported Transaction(s) (Instr. 3 and 4) 6. Ownership Form: Direct (D) or Indirect (I) (Instr. 4) 7. Nature of Indirect Beneficial Ownership (Instr. 4) Code V Amount (A) or (D) Price Common Stock 03/19/2021 P 70,000 ( 1 ) A $ 29 15,393,593 I See Footnote ( 2 ) Common Stock 03/19/2021 P 70,000 ( 3 ) A $ 29 5,859,414 I See Footnote ( 4 ) Common Stock 03/19/2021 P 70,000 ( 5 ) A $ 29 2,633,703 I See Footnote ( 6 ) Common Stock 5,000,000 I See Footnote ( 7 ) Common Stock 3,830,402 I See Footnote ( 8 ) Common Stock 5,789,414 I See Footnote ( 9 )

Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned ( e.g. , puts, calls, warrants, options, convertible securities) 1. Title of Derivative Security (Instr. 3) 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 4. Transaction Code (Instr. 8) 5. Number of Derivative Securities Acquired (A) or Disposed of (D) (Instr. 3, 4, and 5) 6. Date Exercisable and Expiration Date (MM/DD/YY) 7. Title and Amount of Underlying Securities (Instr. 3 and 4) 8. Price of Derivative Security (Instr. 5) 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s) (Instr. 4) 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I) (Instr. 4) 11. Nature of Indirect Beneficial Ownership (Instr. 4) Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other Flagship Ventures Fund IV General Partner LLC 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X Flagship Ventures Fund IV, L.P. 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X Flagship Ventures Fund V General Partner LLC 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X Flagship Ventures Fund V, L.P. 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X Flagship Ventures Opportunities Fund I General Partner LLC 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X Flagship Ventures Opportunities Fund I, L.P. 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X AFEYAN NOUBAR 55 CAMBRIDGE PARKWAY, SUITE 800E CAMBRIDGE, MA02142 X X Signatures Flagship Ventures Fund IV General Partner LLC, By: /s/ Noubar B. Afeyan, Ph.D., Title: Manager 03/23/2021 Signature of Reporting Person Date Flagship Ventures Fund IV, L.P., By: Flagship Ventures Fund IV General Partner LLC, its general partner, By: /s/ Noubar B. Afeyan, Ph.D., Title: Manager 03/23/2021 Signature of Reporting Person Date Flagship Ventures Fund V General Partner LLC, By: /s/ Noubar B. Afeyan, Ph.D., Title: Manager 03/23/2021 Signature of Reporting Person Date Flagship Ventures Fund V, L.P., By: Flagship Ventures Fund V General Partner LLC, its general partner, By: /s/ Noubar B. Afeyan, Ph.D., Title: Manager 03/23/2021 Signature of Reporting Person Date Flagship Ventures Opportunities Fund I General Partner LLC, By: /s/ Noubar B. Afeyan, Ph.D., Title: Manager 03/23/2021 Signature of Reporting Person Date Flagship Ventures Opportunities Fund I, L.P. By: Flagship Ventures Opportunities Fund I General Partner LLC, its general partner, By: /s/ Noubar B. Afeyan, Ph.D., Title: Manager 03/23/2021 Signature of Reporting Person Date Noubar B. Afeyan, Ph.D. By: /s/ Noubar B. Afeyan, Ph.D. 03/23/2021 Signature of Reporting Person Date

Explanation of Responses:

( 1 )On March 19, 2021, Flagship Ventures Fund IV, L.P. ("Flagship Fund IV") acquired 70,000 shares pursuant to an underwritten public offering of common stock by the Issuer (the "Offering"). ( 2 )Shares held by Flagship Fund IV. Flagship Ventures Fund IV General Partner LLC ("Flagship Fund IV GP") is the general partner of Flagship Fund IV. Noubar B. Afeyan, Ph.D. ("Dr. Afeyan") is the sole manager of Flagship Fund IV GP. Each of the reporting persons except for Flagship Fund IV disclaims beneficial ownership of such shares except to the extent of his or its pecuniary interest therein. Edwin M. Kania, Jr. is retired both from Flagship Pioneering, Inc. and as a manager of Flagship Fund IV GP. ( 3 )On March 19, 2021, Flagship Ventures Fund V, L.P. ("Flagship Fund V") acquired 70,000 shares pursuant to the Offering. ( 4 )Shares held by Flagship Fund V. Flagship Ventures Fund V General Partner LLC ("Flagship Fund V GP") is the general partner of Flagship Fund V. Dr. Afeyan is the sole manager of Flagship Fund V GP. Each of the reporting persons except Flagship Fund V disclaims beneficial ownership of such shares except to the extent of his or its pecuniary interest therein. ( 5 )On March 19, 2021, Flagship Ventures Opportunities Fund I, L.P. ("Flagship Opportunities I") acquired 70,000 shares pursuant to the Offering. ( 6 )Shares held by Flagship Opportunities I. Flagship Ventures Opportunities Fund I General Partner LLC ("Flagship Opportunities GP") is the general partner of Flagship Opportunities I. Dr. Afeyan is the sole manager of Flagship Opportunities GP. Each of the reporting persons except for Flagship Opportunities I disclaims beneficial ownership of such shares except to the extent of his or its pecuniary interest therein. ( 7 )Shares held by Flagship VentureLabs IV, LLC ("VentureLabs IV"). Flagship Fund IV is a member of VentureLabs IV and also serves as its manager. Flagship Fund IV GP is the general partner of Flagship Fund IV. Dr. Afeyan is the sole manager of Flagship Fund IV GP. Each of the reporting persons except for VentureLabs IV disclaims beneficial ownership of such shares except to the extent of his or its pecuniary interest therein. ( 8 )Shares held by Flagship Ventures Fund IV-Rx, L.P. ("Flagship Fund IV-Rx"). Flagship Fund IV GP is the general partner of Flagship Fund IV-Rx. Dr. Afeyan is the sole manager of Flagship Fund IV GP. Each of the reporting persons except for Flagship Fund IV-Rx disclaims beneficial ownership of such shares except to the extent of his or its pecuniary interest therein. ( 9 )Shares held by Flagship V VentureLabs Rx Fund, L.P. ("VentureLabs Rx V"). Flagship Fund V GP is the general partner of VentureLabs Rx V. Dr. Afeyan is the sole manager of Flagship Fund V GP. Each of the reporting persons except VentureLabs Rx V disclaims beneficial ownership of such shares except to the extent of his or its pecuniary interest therein.

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.

* If the form is filed by more than one reporting person, see Instruction 4(b)(v).

** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).

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