tl;dr
Understanding how Jira is structured is incredibly important in being able to use it effectively. For example, if you don't understand what a Site it you can get easily mixed up when you're in a new one.
So here we're going to go over how Jira is structured, from the Organization all the way down to the field.
Organization
The organization ("org") is the biggest structure in Jira - however - it's one most folks don't even realize they're interacting with. The organization typically contains every Atlassian product a company uses (although it is possible to have multiple organizations!). Organizations provide a layer that controls things like licensing, billing and security.
Organizations are managed by Org Administrations (Org Admins). Typically a company will have a small number of these folks, and they're responsible for managing things like billing, access and the like.
Site
The site is the next layer down and contains various Applications ("Apps") - although each Atlassian App can only appear once per site. For example, your organization may have a site called "EuropeTeam" that has Jira and Confluence, and another site that is called "AfricaTeam" that only has Jira. In the screenshot about we're looking at the "one-atlas-tecz" site.
Sites allow company's to control apps at a broad level, and each one has it's own URL. The URL, by default, uses (name).atlassian.net. For example "jayquill.atlassian.net" is a site, although Org admins can use a custom URL instead (e.g. "jayquill.com").
There is a Site admin who is responsible for just their site - although if there's only one site the Org admin is also the site admin.
Note that if your company has multiple sites you may have to log into multiple apps (more on that below).
App (Jira)
When you click a login link you'll end up in the App, and this is what most people interact with when they access Jira. Keep in mind that every App is different, so as you change jobs you'll end up working in different apps (this confused the heck out of me when I changes jobs since I didn't realize the configuration can differ!).
Jira is maintained by a Jira Admin - the person responsible for configuration of various Jira settings (like Schemes, workflows and the like). I highly recommend you figure out who your company's Jira Admin(s) is as they typically know a lot about Jira and can help you out (especially if you do something silly, like, accidentally delete 10k work items...).
This level also contains all of the permissions and access you'll be using to interact with Jira (which is one reason you should befriend your Jira admin!). This is also where all of the spaces and work items you interact with will live.
If your company has multiple sites you may end up in multiple Apps. Keep in mind apps are entirely separate from each other - so work and configurations that exist in one doesn't necessarily exist in another.
Space (Formerly "Project")
A space is a container within Jira that lets you organize work items. I think of spaces like a room in a building - it's just a room, what I put in it is what's important. That said, spaces have a number of features that can be configured and used to manage work. For example one space may have a Kanban board, while another uses a calendar view.
There are two kinds of spaces - team and company managed. At a high level team managed spaces offer less features but more control to space admins, while company managed projects are more sophisticated but require a Jira admin for much of the config.
Spaces are maintained by space admins (another good person for you to get to know). Space admins have wide (but limited) control to manage their space. In a team managed project they will have much greater ability to control configuration than a company-managed project, so keep in mind they may not be able to immediately adjust something.
Work Item (Formerly "Issue")
The work item is what you'll be spending most of your time staring it. It's the digital representation of your work. This could be to write some code, debug some code, write a report, onboard a worker, clean a room, pay your taxes, basically anything. Regardless of what they represent work items live in one, and only one, space (although they can be moved between them).
Depending on their type (e.g. "bug", "task", "something you made up") work items will have different settings - primarily workflows and fields (more on those below). Workflows are the series of statuses a work item moves through (e.g. "new", "in progress", "done", "I forgot about this one"). Workflows should help support the processes your team uses to accomplish work and are typically controlled by a Jira Admin (in company managed spaces) or a space admin (in team managed ones).
Fields
Fields are the pieces of information attached to a work item. Some are always mandatory (key, summary) while others are optional. Jira comes with a LOT of fields out of the box, but you can also add custom fields depending on what your team needs to do.
The fields available on a work item are also dependent on how the work type is setup - so it is very likely you'll see fields appear or disappear when you change work items (this confused the heck out of me before I knew what was going on!).
Additional Info
Check out these links for more!
Robert Hean
Systems Manager & Trainer
Hean
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