Jalview shows MSA and structure alignment with Jmol. Jalview could also link to iCn3D to show MSA with all or a subset of structures.
One example with the MSA file "GPCR.aln" is shown here. It could be reproduced with a short URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/share2.html?8f6858c412b45e08fe992d5f854bb4e5 or full URL: https://www.ncbi.nlm.nih.gov/Structure/icn3d/full_3.45.0.html?date=20250711&v=3.45.0&command=load+mmdbaf0+3SN6,1GZM,4DAJ,4U15,3UON,4MQS,5DSG,4DKL,4DJH,2RH1,5CXV,4EJ4,4IAR,2VT4,3PBL,4EA3,3RZE,4NC3,3ODU,4MBS,4GRV,3EML,3QAK,3V2Y,3PQR,2X72,3VW7;+realign+predefined+3SN6_R,1GZM_A,4DAJ_A,4U15_A,3UON_A,4MQS_A,5DSG_A,4DKL_A,4DJH_A,2RH1_A,5CXV_A,4EJ4_A,4IAR_A,2VT4_B,3PBL_B,4EA3_A,3RZE_A,4NC3_A,3ODU_A,4MBS_A,4GRV_A,3EML_A,3QAK_A,3V2Y_A,3PQR_A,2X72_A,3VW7_A+1131-1160,30-144,146-175,184-239,265-341+%7C+0-29,34-178,181-190,198-282,284-307,309-322:+30-175,183-239,265-268,272-338+%7C+64-209,213-223,225-259,1001-1011,482-485,489-544,546-556:+30-175,183-239,265-339+%7C+64-209,213-223,225-259,1001-1011,482-544,546-557:+30-138,140-175,183-239,265-341+%7C+20-134,136-165,169-179,181-217,1002-1010,379-441,443-456:+30-175,183-228,265-341+%7C+20-165,169-179,181-215,379-441,443-456:+1156-1160,30-138,140-175,183-239,269-341+%7C+20-24,29-143,145-174,178-188,190-226,1002-1010,396-454,456-469:+30-84,86-138,140-175,185-239,265-341+%7C+65-178,180-209,212-220,227-263,1002-1010,272-310,314-337,339-352:+30-84,86-175,184-239,265-300,304-341+%7C+56-200,204-213,221-261,1002-1006,266-301,308-331,333-346:+30-175,179-192,194-239,265-341+%7C+30-175,179-180,182-230,1002-1010,265-341:+30-175,183-205,207-239,265-341+%7C+22-167,171-181,184-218,1001-1010,357-419,421-434:+1160,30-84,86-138,140-175,185-239,265-335+%7C+41,46-159,161-190,193-201,208-244,1002-1010,253-291,296-319,321-328:+1157-1160,30-174,188-239,265-298,304-341+%7C+38-41,46-190,197-239,1001-1009,306-339,347-370,372-385:+31-144,146-175,179-192,194-230,267-341+%7C+39-147,149-183,187-188,190-238,284-344,346-359:+36-138,146-175,186-192,195-239,265-341+%7C+32-92,94-135,146-175,177-221,1002-1008,321-359,361-384,386-399:+30-84,86-138,146-175,185-238,265-337+%7C+48-155,163-192,195-203,210-293,297-320,322-331:+34-138,140-173,185-239,265-341+%7C+28-138,140-167,175-183,185-221,1002-1010,407-469,471-484:+30-175,184-239,265-341+%7C+51-117,119-197,201-210,212-248,1001-1009,316-354,358-381,383-396:+1157-1160,30-86,89-144,146-175,185-239,265-341+%7C+27-30,35-157,159-178,181-189,194-229,900-901,1002-1009,231-269,280-303,305-318:+1157-1160,30-84,86-96,98-138,140-175,185-239,265-341+%7C+19-22,27-139,141-170,173-181,189-223,1001-1011,227-265,275-298,300-313:+1156-1160,30-61,63-175,179-180,182-239,265-335+%7C+52-56,61-92,97-130,133-211,215-228,232-268,1002-1010,300-338,347-370,372-379:+30-95,98-138,140-175,181-239,265-341+%7C+3-115,117-146,157-169,172-208,1002-1010,225-263,266-289,291-304:+30-95,98-138,140-175,182-239,265-341+%7C+3-115,117-146,158-169,172-208,1002-1010,225-263,266-289,291-304:+1138-1160,30-45,47-90,92-137,146-175,184-192,195-205,207-239,265-341+%7C+16-38,43-148,156-185,189-231,1002-1011,248-286,289-312,314-327:+1132-1160,30-144,146-175,184-239,265-341+%7C+1-29,34-178,181-190,198-282,284-307,309-322:+1131-1160,30-144,146-175,184-239,265-341+%7C+0-29,34-178,181-190,198-282,284-307,309-322:+1157-1160,30-84,86-139,145-175,184-239,265-331+%7C+91-94,99-164,166-208,214-244,248-257,265-301,1002-1010,305-343,349-372,375-378;+color+identity;+defined+sets;+select+sets+1GZM_A+or+4DAJ_A+or+4U15_A;+show+selection%7C%7C%7C%7B%22factor%22:%221.000%22,%22mouseChange%22:%7B%22x%22:%220.000%22,%22y%22:%220.000%22%7D,%22quaternion%22:%7B%22_x%22:%22-0.2299%22,%22_y%22:%220.6529%22,%22_z%22:%22-0.6038%22,%22_w%22:%220.3955%22%7D%7D
