diff --git a/pkgs/applications/misc/ola/default.nix b/pkgs/applications/misc/ola/default.nix
index 792cff81865..fce6b8426cb 100644
--- a/pkgs/applications/misc/ola/default.nix
+++ b/pkgs/applications/misc/ola/default.nix
@@ -16,7 +16,10 @@ stdenv.mkDerivation rec {
 
   nativeBuildInputs = [ autoreconfHook bison flex pkgconfig perl ];
   buildInputs = [ libuuid cppunit protobuf3_1 zlib avahi libmicrohttpd python3 ];
-  propagatedBuildInputs = [ python3Packages.protobuf3_1 python3Packages.numpy ];
+  propagatedBuildInputs = [
+    (python3Packages.protobuf.override { protobuf = protobuf3_1; })
+    python3Packages.numpy
+  ];
 
   configureFlags = [ "--enable-python-libs" ];
 
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 018bba2aff8..b62d820e35f 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -21679,14 +21679,14 @@ with pkgs;
     inherit (darwin.apple_sdk.frameworks) Accelerate CoreGraphics CoreVideo;
   };
 
-  caffe2 = callPackage ../development/libraries/science/math/caffe2 {
+  caffe2 = callPackage ../development/libraries/science/math/caffe2 (rec {
     eigen3 = eigen3_3;
     inherit (python3Packages) python future six numpy pydot;
     protobuf = protobuf3_1;
-    python-protobuf = python3Packages.protobuf3_1;
+    python-protobuf = python3Packages.protobuf.override { inherit protobuf; };
     # Used only for image loading.
     opencv3 = opencv3WithoutCuda;
-  };
+  });
 
   cntk = callPackage ../applications/science/math/cntk rec {
     cudaSupport = pkgs.config.cudaSupport or false;
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index e4e561682bf..1a03ea3ad0b 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -3771,12 +3771,6 @@ in {
     protobuf = pkgs.protobuf;
   };
 
-  protobuf3_1 = callPackage ../development/python-modules/protobuf {
-    disabled = isPyPy;
-    doCheck = !isPy3k;
-    protobuf = pkgs.protobuf3_1;
-  };
-
   psd-tools = callPackage ../development/python-modules/psd-tools { };
 
   psutil = callPackage ../development/python-modules/psutil { };