Japan proper has four main islands, which are (from north to south) Hokkaido, Honshu (the largest island, where the capital and most major cities are located), Shikoku, and Kyushu. There are also many smaller islands stretched in an arc between the Sea of Japan and the East China Sea and the Pacific proper. Honshu, Shikoku, and Kyushu enclose the Inland Sea. The general features of the four main islands are shapely mountains, sometimes snowcapped, the highest and most famous of which is sacred Mt. Fuji; short rushing rivers; forested slopes; irregular and lovely lakes; and small, rich plains. Mountains, many of them volcanoes, cover two thirds of Japan's surface, hampering transportation and limiting agriculture.

On the arable land, which is only 11% of Japan's total land area, the population density is among the highest in the world. The climate ranges from chilly humid continental to humid subtropical. Rainfall is abundant, and typhoons and earthquakes are frequent. (For a more detailed description of geography, see separate articles on the individual islands.) Mineral resources are meager, except for coal, which is an important source of industrial energy. The rapid streams supply plentiful hydroelectric power. Imported oil, however, is the major source of energy. Prior to 2011, one third of Japan's electricity came from nuclear power, but following the post-tsunami cooling failures at the Fukushima No. 1 power plant that year all reactors were gradually brought offline for maintenance and safety testing. Operations began resuming in Aug., 2015. The rivers are generally unsuited for navigation (only two, the Ishikari and the Shinano, are over 200 mi/322 km long), and railroads and ships along the coast are the chief means of transportation. The Shinkansen bullet train, the second-fastest train system in the world after France's TGV, was inaugurated in 1964 between Tokyo and Osaka and later extended.

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