The shooting came when hundreds of Morsi supporters marched on the Guard building, where Morsi was staying at the time of his ouster before being taken into military custody in an unknown location. The crowd approached a barbed wire barrier where troops were standing guard around the building.
When one supporter hung a sign of Morsi on the barrier, the troops tore it down and told the crowd to stay back. A protester hung a second sign and the soldiers opened fire on the crowd, an Associated Press photographer at the scene said. Several protesters were wounded, many with the pockmark wounds typical of birdshot.
At least one had a gaping, bleeding exit wound in the back of his head. Fellow protesters carried the body into a nearby building and covered his head with a blanket, declaring him dead, according to AP Television News footage. Health Ministry official Khaled el-Khatib confirmed that one protester was killed Friday and a number wounded, but he did not know the exact number.
Protesters pelted the line of troops with stones, and the soldiers responded with volleys of tear gas, but the clashes appeared for the moment to ease with mid-afternoon prayers.
The shooting risks to escalate Egypt's confrontation, with supporters of Morsi - largely Islamists - rejecting the army's ousting of the country's first freely elected president Wednesday night and installation of a new civilian administration. The protester casualties are likely to further fuel calls by some in the Islamist movement for violent retaliation.
The first major Islamic militant attack came before dawn Friday in the tumultuous Sinai Peninsula, killing at least one soldier. Masked assailants launched a coordinated attack with rockets, rocket-propelled grenades and anti-aircraft guns on the airport in el-Arish, the provincial capital of northern Sinai, as well as a security forces camp in Rafah on the border with Gaza and five other military and police posts, sparking nearly four hours of clashes.
One of military's top commanders, Gen. Ahmed Wasfi arrived at el-Arish on Friday to lead operations there as the army declared a "war on terrorism" in Sinai. A crowd of Morsi supporters tried to storm the governor's office in the city but were dispersed by security forces.
The Brotherhood called for Friday's protests, which took place at several sites around the capital and in other cities. Brotherhood officials underlined strongly to their followers that their rallies should be peaceful.
A crowd of tens of thousands of Morsi supporters filled much of a broad boulevard outside a Cairo mosque several blocks away from the Republican Guard headquarters, vowing to remain in place until Morsi is restored. The protesters railed against what they called the return of the regime of autocrat Hosni Mubarak, ousted in early 2011.
"The old regime has come back ... worse than before," said Ismail Abdel-Mohsen, an 18-year old student among the crowds outside the Rabia al-Adawiya Mosque. He dismissed the new interim head of state sworn in a day earlier, senior judge Adly Mansour, as "the military puppet."
"After sunset, President Morsi will be back in the palace," they chanted. "The people want God's law. Islamic, Islamic, whether the army likes it or not."
The military forced Morsi out Wednesday after millions of Egyptians turned out in four days of protests demanding his removal and saying he had squandered his electoral mandate by putting power in the hands of his own Muslim Brotherhood and other, harder-line Islamists. In the 48 hours since, the military has moved against the Brotherhood's senior leadership, putting Morsi under detention and arresting the group's supreme leader and a string of other figures.
On Friday, Mansour dissolved the country's interim parliament - the upper house of the legislature, which was overwhelmingly dominated by Islamists and Morsi allies. The Shura Council, which normally does not legislate, held legislative powers under Morsi's presidency because the lower house had been dissolved. State Tv reported Mansour's constitutional decree dissolving the body but did not give further details.
Mansour also named the head of General Intelligence, Rafaat Shehata, as his security adviser.
Morsi supporters say the military has wrecked Egypt's democracy by carrying out a coup against an elected leader. They accuse Mubarak loyalists and liberal and secular opposition parties of turning to the army for help because they lost at the polls to Islamists.
But many supporters have equally seen it as a conspiracy against Islam.
Many at Friday's protests held copies of the Quran in the air, and much of the crowd had the long beards of ultraconservative men or encompassing black robes and veils worn by women, leaving only the eyes visible. One protester shouted that the sheik of Al-Azhar - Egypt's top Muslim cleric who backed the military's move - was "an agent of the Christians" - reflecting a sentiment that the Christian minority was behind Morsi's ouster.
The protesters set up "self-defense" teams, with men staffing checkpoints touting sticks and home-made body shields. There was no significant presence of military forces near the protests.
In southern Egypt, Islamists attacked the main church in the city of Qena on Friday. In the town of Dabaiya near the city of Luxor, a mob torched houses of Christians, sending dozens of Christians seeking shelter in a police station. Clashes broke out Friday in at least two cities in the Nile Delta between pro- and anti-Morsi demonstrators.
Extremist groups who gained considerable influence during Morsi's year in office have threatened to lash out with a campaign of violence.
Islamic militants hold a powerful sway in the lawless and chaotic northern Sinai. They are heavily armed with weapons smuggled from Libya and have links with militants in the neighboring Gaza Strip, run by Hamas. After the attack, Egypt indefinitely closed its border crossing into Gaza, sending 200 Palestinians back into the territory, said Gen. Sami Metwali, director of Rafah passage.
The night before, the military spokesman issued a statement urging all protesters to remain peaceful. In a message to Morsi's opponents, Col. Ahmed Mohammed Ali warned against "gloating," vengeance or attacks on Brotherhood offices, saying there must not be an "endless cycle of revenge."
The military has a "strong will to ensure national reconciliation, constructive justice and tolerance," he wrote in an official Facebook posting. He said the army and security forces will not take "any exceptional or arbitrary measures" against any political group.
But the Brotherhood has been furious over the arrests of its top leaders, as well as the closure of its TV station Misr25, its newspaper, and three other Islamist television stations. It called to move a return to Egypt's " dark, repressive, dictatorial and corrupt ages."
"We refuse to participate in any activities with the usurping authorities," the Brotherhood said in a statement, read Thursday by senior cleric Abdel-Rahman el-Barr to the crowd outside the Rabia al-Adawiya Mosque.
The first steps for creating a post-Morsi government were taken Thursday, when Mansour, the 67-year-old chief justice of the Supreme Constitutional Court, was sworn in by fellow judges as interim president. A Cabinet of technocrats is to be formed to run the country for an interim period until new elections can be held - though officials have not said how long that will be. In the meantime, the Islamist-written constitution has been suspended.
Morsi has been under detention in an unknown location since Wednesday night, and at least a dozen of his top aides and advisers have been under what is described as "house arrest," though their locations are also unknown.
Besides the Brotherhood's top leader, General Guide Mohammed Badie, security officials have also arrested his predecessor, Mahdi Akef, and one of his two deputies, Rashad Bayoumi, as well as Saad el-Katatni, head of the Brotherhood's Freedom and Justice Party, and ultraconservative Salafi figure Hazem Abu Ismail, who has a considerable street following.
Authorities have also issued a wanted list for more than 200 Brotherhood members and leaders of other Islamist groups. Among them is Khairat el-Shater, another deputy of the general guide who is widely considered the most powerful figure in the Brotherhood.
The arrest of Badie was a dramatic step, since even Mubarak and his predecessors had been reluctant to move against the group's top leader. The ranks of Brotherhood members across the country swear a strict oath of unquestioning allegiance to the general guide, vowing to "hear and obey." It has been decades since a Brotherhood general guide was put in a prison.
Badie and el-Shater were widely believed by the opposition to be the real power in Egypt during Morsi's term.
The National Salvation Front, the top opposition political group during Morsi's presidency and a key member of the coalition that worked with the military in his removal, criticized the moves, saying, "We totally reject excluding any party, particularly political Islamic groups."
The Front has proposed one of its top leaders, Mohammed ElBaradei, to become prime minister of the interim Cabinet, a post that will hold strong powers since Mansour's presidency post is considered symbolic. ElBaradei, a Nobel Peace laureate who once headed the U.N. nuclear watchdog agency, is considered Egypt's top reform advocate.
"Reconciliation is the name of the game, including the Muslim Brotherhood. We need to be inclusive," Munir Fakhry Abdel-Nour, a leading member of the group, told The Associated Press. "The detentions are a mistake."
AP correspondent Sarah El Deeb contributed to this report.