How to write a CV for a PhD application
Academic CVs vary quite a bit from a traditional CV in ways that will help you illuminate your research experience. While there are plenty of (conflicting) guidelines about how to structure or format an academic CV, the following sections are generally included (if you are at the stage of your career that they are relevant), not necessarily in the order below:


Basic demographic information (name, contact address, possibly birthdate and marital status and photograph, depending on the country)
Brief statement of your research area/interests/objectives
Degrees obtained/in-progress (institution, supervisor, thesis title, GPA)
Academia-relevant jobs (e.g., research assistantships, teaching assistantships, tenure-track appointments)
Publications (especially in the case of junior researchers, also papers that are under review/in submission)
Awards or honors or grants
Teaching experience (including in labs, if you are a junior researcher)
Supervisory experience (if you have helped co-supervise other students)
Service (reviewing duties, committees on which you've served, organization of workshops/conferences, editorial work)
Research project experience (where you can outline work that you have done in a research lab)
Presentations and seminars (especially if you have been to any conferences or workshops)
International network (if it is important to show that you have international collaborators)
References (presumably your previous supervisors)


In your case, specifically, the fact that you will have submitted the paper is quite important, because at that stage you can list it as a paper (under review) on your CV. 

Regarding your masters thesis, you can indicate a working title for your thesis when you list your Masters under your education. This implies research experience and the area in which the experience has been acquired. You can furthermore describe under your research project experience what skills/roles you have had in the lab in which you have conducted your Masters research. (You can also indicate here your summer internship, since it sounds like it was research-focused.)

Furthermore, you can highlight the especially salient points again in your cover letter, especially if there are elements of your Masters experience that relate to the specific PhD programme to which you are applying.