Not sure whether this is the right solution. I experimented by adding content to the Modules/Setup.local. After adding the _struct line, the original error went away. Eventually using a file like:
# Edit this file for local setup changes
#*shared*
#readline readline.c -lreadline -ltermcap
# Modules that should always be present (non UNIX dependent):
array arraymodule.c # array objects
cmath cmathmodule.c _math.c # -lm # complex math library functions
math mathmodule.c _math.c # -lm # math library functions, e.g. sin()
_struct _struct.c # binary structure packing/unpacking
time timemodule.c # -lm # time operations and variables
operator operator.c # operator.add() and similar goodies
#_testcapi _testcapimodule.c # Python C API test module
_random _randommodule.c # Random number generator
_collections _collectionsmodule.c # Container types
_heapq _heapqmodule.c # Heapq type
itertools itertoolsmodule.c # Functions creating iterators for efficient looping
strop stropmodule.c # String manipulations
_functools _functoolsmodule.c # Tools for working with functions and callable objects
_elementtree -I$(srcdir)/Modules/expat -DHAVE_EXPAT_CONFIG_H -DUSE_PYEXPAT_CAPI _elementtree.c # elementtree accelerator
#_pickle _pickle.c # pickle accelerator
datetime datetimemodule.c # date/time type
_bisect _bisectmodule.c # Bisection algorithms
unicodedata unicodedata.c # static Unicode character database
# access to ISO C locale support
#_locale _localemodule.c # -lintl
# Standard I/O baseline
_io -I$(srcdir)/Modules/_io _io/bufferedio.c _io/bytesio.c _io/fileio.c _io/iobase.c _io/_iomodule.c _io/stringio.c _io/textio.c
# added due to missing for virtualenv:
binascii binascii.c
cStringIO cStringIO.c
cPickle cPickle.c
# Modules with some UNIX dependencies -- on by default:
fcntl fcntlmodule.c # fcntl(2) and ioctl(2)
spwd spwdmodule.c # spwd(3)
grp grpmodule.c # grp(3)
select selectmodule.c # select(2); not on ancient System V
# Memory-mapped files (also works on Win32).
mmap mmapmodule.c
# CSV file helper
_csv _csv.c
# Socket module helper for socket(2)
_socket socketmodule.c timemodule.c
# Some more UNIX dependent modules -- off by default, since these
# are not supported by all UNIX systems:
#nis nismodule.c -lnsl # Sun yellow pages -- not everywhere
termios termios.c # Steen Lumholt's termios module
resource resource.c # Jeremy Hylton's rlimit interface
# Note that the _md5 and _sha modules are normally only built if the
# system does not have the OpenSSL libs containing an optimized version.
# The _md5 module implements the RSA Data Security, Inc. MD5
# Message-Digest Algorithm, described in RFC 1321. The necessary files
# md5.c and md5.h are included here.
_md5 md5module.c md5.c
# The _sha module implements the SHA checksum algorithms.
# (NIST's Secure Hash Algorithms.)
_sha shamodule.c
_sha256 sha256module.c
_sha512 sha512module.c
# Andrew Kuchling's zlib module.
# This require zlib 1.1.3 (or later).
# See http://www.gzip.org/zlib/
zlib zlibmodule.c -I$(prefix)/include -L$(exec_prefix)/lib -lz
