The variable size and shape of HIV has made it hard to map, the team said in the journal Structure.
So the UK-German team took hundreds of images of viruses, that are 60 times smaller than red blood cells, and used a computer program to combine them.
Oxford University's Professor Stephen Fuller said the 3D map would assist in understanding how the virus grows.
Unusual features
He told the BBC: "You say can you show me the structure of the HIV virus and the question is which one.
"HIV is very variable. It varied in diameter by a factor of three."
The way the research team, from the Wellcome Trust Centre for Human Genetics at Oxford University, dealt with this was by taking multiple images at different tilts.
Working with colleagues in Heidelberg and Munich, they took about 100 images of 70 individual HIV viruses and then looked at similarities.
Despite the variability, the team found some consistent features.
T cells
This included the finding that the core of virus - which is cone-shaped - spans the width of the viral membrane.
But there are spikes on the outside which bind to human immune cells, called T cells, and allow the virus to invade them.
The significance of this is that whereas most viruses have internal structures which define the size, in the HIV virus it is the membrane which defines the size.
"This could inform the development of more effective therapeutic approaches"
This puts constraints on the way it can assemble, the team said.
Professor Fuller said: "Identifying how the virus grows will allow us to address the formation of this important pathogen and how it accommodates its variability.
"This could inform the development of more effective therapeutic approaches," he added.
But Professor Fuller, who continues to work on HIV, acknowledges that a new HIV vaccine or treatment resulting from his research was a long way off.
But he says the research could provide an insight into the way to prevent the virus from assembling.
Treatments?
Like any virus, HIV is not a cell but rather strands of genetic code wrapped in protein.
The virus invades living cells and take them over by usurping the cell's genetic code with its own.
Roger Pebody, treatment specialist at HIV/Aids charity Terrence Higgins Trust, said: "Revealing the 3D structure of HIV may not sound very exciting but it's actually really useful, giving us more information about the virus and how it grows.
"The more we understand about HIV, the more likely we are to be able to develop effective treatments and hopefully one day a cure."
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