{"bundle_type":"pith_open_graph_bundle","bundle_version":"1.0","pith_number":"pith:2026:4M2CALQHXU7XLQXVJK7FLFGNUF","short_pith_number":"pith:4M2CALQH","canonical_record":{"source":{"id":"2605.30518","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2026-05-28T19:55:17Z","cross_cats_sorted":[],"title_canon_sha256":"9a169b7ce946e5998e00ee34771c2b6ccc303836e39e395c1de82f12c3a18101","abstract_canon_sha256":"abb20cd9be1dc0a04b56b83c9513696c38509ead6c42ef73bc26d898f0e569cd"},"schema_version":"1.0"},"canonical_sha256":"e334202e07bd3f75c2f54abe5594cda140678021c0971ba7a45482edb038f21a","source":{"kind":"arxiv","id":"2605.30518","version":1},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2605.30518","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"arxiv_version","alias_value":"2605.30518v1","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2605.30518","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"pith_short_12","alias_value":"4M2CALQHXU7X","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"pith_short_16","alias_value":"4M2CALQHXU7XLQXV","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"pith_short_8","alias_value":"4M2CALQH","created_at":"2026-06-01T01:02:58Z"}],"events":[{"event_type":"record_created","subject_pith_number":"pith:2026:4M2CALQHXU7XLQXVJK7FLFGNUF","target":"record","payload":{"canonical_record":{"source":{"id":"2605.30518","kind":"arxiv","version":1},"metadata":{"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2026-05-28T19:55:17Z","cross_cats_sorted":[],"title_canon_sha256":"9a169b7ce946e5998e00ee34771c2b6ccc303836e39e395c1de82f12c3a18101","abstract_canon_sha256":"abb20cd9be1dc0a04b56b83c9513696c38509ead6c42ef73bc26d898f0e569cd"},"schema_version":"1.0"},"canonical_sha256":"e334202e07bd3f75c2f54abe5594cda140678021c0971ba7a45482edb038f21a","receipt":{"kind":"pith_receipt","key_id":"pith-v1-2026-05","algorithm":"ed25519","signed_at":"2026-06-01T01:02:58.692222Z","signature_b64":"CsUIzId83sBs9jLurSbiLqi+9IwyIoY/lNq/BoZ6xdXFRYUoH1VwtC9iEQTHrLOUzI7DNniuTPKEZBvQOSTSBA==","signed_message":"canonical_sha256_bytes","builder_version":"pith-number-builder-2026-05-17-v1","receipt_version":"0.3","canonical_sha256":"e334202e07bd3f75c2f54abe5594cda140678021c0971ba7a45482edb038f21a","last_reissued_at":"2026-06-01T01:02:58.691342Z","signature_status":"signed_v1","first_computed_at":"2026-06-01T01:02:58.691342Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"source_kind":"arxiv","source_id":"2605.30518","source_version":1,"attestation_state":"computed"},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-06-01T01:02:58Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"HaYn9L17D9idRJGvBd6Rshq6Ftj8/xXgnPm+6D2i4KGa7aMeJJNtnF3zIYB4idz21uxShRtjOCxzIMPiFQdTDg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-03T03:31:24.751102Z"},"content_sha256":"732065a66665a3fdb513f488bf20dc16a7e34896c006545ac7a0af2bde3c137e","schema_version":"1.0","event_id":"sha256:732065a66665a3fdb513f488bf20dc16a7e34896c006545ac7a0af2bde3c137e"},{"event_type":"graph_snapshot","subject_pith_number":"pith:2026:4M2CALQHXU7XLQXVJK7FLFGNUF","target":"graph","payload":{"graph_snapshot":{"paper":{"title":"Gaussian Mixture Model-Based Focused Refinement for Enhanced Flexible Structure Determination in CryoEM and CryoET","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":[],"primary_cat":"q-bio.QM","authors_text":"Muyuan Chen","submitted_at":"2026-05-28T19:55:17Z","abstract_excerpt":"Dynamic conformational changes of proteins are crucial for their cellular functions. Here we present a unified refinement pipeline for flexible protein structures in both CryoEM and in situ CryoET. Using a Gaussian mixture model-based focused alignment procedure, we improve resolution of small domains in highly dynamic proteins and reveal intricate conformational changes. The method corrects the per-subunit motion of TRPV1 and captures the rotary dynamics of ATP synthase within mitochondria."},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.30518","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2605.30518/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"},"verdict_id":null},"signer":{"signer_id":"pith.science","signer_type":"pith_registry","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54"},"created_at":"2026-06-01T01:02:58Z","supersedes":[],"prev_event":null,"signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"LIxTZ6HandVdHVH67tiPkQg6m1deEcDI8jWd1IwMR/pr55uoT6y2JfvAQe1LnYjYQ2IsYTOxdr8RXvA4TTxyBg==","signed_message":"open_graph_event_sha256_bytes","signed_at":"2026-07-03T03:31:24.751481Z"},"content_sha256":"3786e74bd102d980739dc51031e46f2676a7de47f4c5de4679c9b547778f7dc3","schema_version":"1.0","event_id":"sha256:3786e74bd102d980739dc51031e46f2676a7de47f4c5de4679c9b547778f7dc3"}],"timestamp_proofs":[],"mirror_hints":[{"mirror_type":"https","name":"Pith Resolver","base_url":"https://pith.science","bundle_url":"https://pith.science/pith/4M2CALQHXU7XLQXVJK7FLFGNUF/bundle.json","state_url":"https://pith.science/pith/4M2CALQHXU7XLQXVJK7FLFGNUF/state.json","well_known_bundle_url":"https://pith.science/.well-known/pith/4M2CALQHXU7XLQXVJK7FLFGNUF/bundle.json","status":"primary"}],"public_keys":[{"key_id":"pith-v1-2026-05","algorithm":"ed25519","format":"raw","public_key_b64":"stVStoiQhXFxp4s2pdzPNoqVNBMojDU/fJ2db5S3CbM=","public_key_hex":"b2d552b68890857171a78b36a5dccf368a953413288c353f7c9d9d6f94b709b3","fingerprint_sha256_b32_first128bits":"RVFV5Z2OI2J3ZUO7ERDEBCYNKS","fingerprint_sha256_hex":"8d4b5ee74e4693bcd1df2446408b0d54","rotates_at":null,"url":"https://pith.science/pith-signing-key.json","notes":"Pith uses this Ed25519 key to sign canonical record SHA-256 digests. Verify with: ed25519_verify(public_key, message=canonical_sha256_bytes, signature=base64decode(signature_b64))."}],"merge_version":"pith-open-graph-merge-v1","built_at":"2026-07-03T03:31:24Z","links":{"resolver":"https://pith.science/pith/4M2CALQHXU7XLQXVJK7FLFGNUF","bundle":"https://pith.science/pith/4M2CALQHXU7XLQXVJK7FLFGNUF/bundle.json","state":"https://pith.science/pith/4M2CALQHXU7XLQXVJK7FLFGNUF/state.json","well_known_bundle":"https://pith.science/.well-known/pith/4M2CALQHXU7XLQXVJK7FLFGNUF/bundle.json"},"state":{"state_type":"pith_open_graph_state","state_version":"1.0","pith_number":"pith:2026:4M2CALQHXU7XLQXVJK7FLFGNUF","merge_version":"pith-open-graph-merge-v1","event_count":2,"valid_event_count":2,"invalid_event_count":0,"equivocation_count":0,"current":{"canonical_record":{"metadata":{"abstract_canon_sha256":"abb20cd9be1dc0a04b56b83c9513696c38509ead6c42ef73bc26d898f0e569cd","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2026-05-28T19:55:17Z","title_canon_sha256":"9a169b7ce946e5998e00ee34771c2b6ccc303836e39e395c1de82f12c3a18101"},"schema_version":"1.0","source":{"id":"2605.30518","kind":"arxiv","version":1}},"source_aliases":[{"alias_kind":"arxiv","alias_value":"2605.30518","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"arxiv_version","alias_value":"2605.30518v1","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"doi","alias_value":"10.48550/arxiv.2605.30518","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"pith_short_12","alias_value":"4M2CALQHXU7X","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"pith_short_16","alias_value":"4M2CALQHXU7XLQXV","created_at":"2026-06-01T01:02:58Z"},{"alias_kind":"pith_short_8","alias_value":"4M2CALQH","created_at":"2026-06-01T01:02:58Z"}],"graph_snapshots":[{"event_id":"sha256:3786e74bd102d980739dc51031e46f2676a7de47f4c5de4679c9b547778f7dc3","target":"graph","created_at":"2026-06-01T01:02:58Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"graph_snapshot":{"author_claims":{"count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","strong_count":0},"builder_version":"pith-number-builder-2026-05-17-v1","claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"integrity":{"available":true,"clean":true,"detectors_run":[],"endpoint":"/pith/2605.30518/integrity.json","findings":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938","summary":{"advisory":0,"by_detector":{},"critical":0,"informational":0}},"paper":{"abstract_excerpt":"Dynamic conformational changes of proteins are crucial for their cellular functions. Here we present a unified refinement pipeline for flexible protein structures in both CryoEM and in situ CryoET. Using a Gaussian mixture model-based focused alignment procedure, we improve resolution of small domains in highly dynamic proteins and reveal intricate conformational changes. The method corrects the per-subunit motion of TRPV1 and captures the rotary dynamics of ATP synthase within mitochondria.","authors_text":"Muyuan Chen","cross_cats":[],"headline":"","license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2026-05-28T19:55:17Z","title":"Gaussian Mixture Model-Based Focused Refinement for Enhanced Flexible Structure Determination in CryoEM and CryoET"},"references":{"count":0,"internal_anchors":0,"resolved_work":0,"sample":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.30518","kind":"arxiv","version":1},"verdict":{"created_at":null,"id":null,"model_set":{},"one_line_summary":"","pipeline_version":null,"pith_extraction_headline":"","strongest_claim":"","weakest_assumption":""}},"verdict_id":null}}],"author_attestations":[],"timestamp_anchors":[],"storage_attestations":[],"citation_signatures":[],"replication_records":[],"corrections":[],"mirror_hints":[],"record_created":{"event_id":"sha256:732065a66665a3fdb513f488bf20dc16a7e34896c006545ac7a0af2bde3c137e","target":"record","created_at":"2026-06-01T01:02:58Z","signer":{"key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signer_id":"pith.science","signer_type":"pith_registry"},"payload":{"attestation_state":"computed","canonical_record":{"metadata":{"abstract_canon_sha256":"abb20cd9be1dc0a04b56b83c9513696c38509ead6c42ef73bc26d898f0e569cd","cross_cats_sorted":[],"license":"http://creativecommons.org/licenses/by/4.0/","primary_cat":"q-bio.QM","submitted_at":"2026-05-28T19:55:17Z","title_canon_sha256":"9a169b7ce946e5998e00ee34771c2b6ccc303836e39e395c1de82f12c3a18101"},"schema_version":"1.0","source":{"id":"2605.30518","kind":"arxiv","version":1}},"canonical_sha256":"e334202e07bd3f75c2f54abe5594cda140678021c0971ba7a45482edb038f21a","receipt":{"algorithm":"ed25519","builder_version":"pith-number-builder-2026-05-17-v1","canonical_sha256":"e334202e07bd3f75c2f54abe5594cda140678021c0971ba7a45482edb038f21a","first_computed_at":"2026-06-01T01:02:58.691342Z","key_id":"pith-v1-2026-05","kind":"pith_receipt","last_reissued_at":"2026-06-01T01:02:58.691342Z","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","receipt_version":"0.3","signature_b64":"CsUIzId83sBs9jLurSbiLqi+9IwyIoY/lNq/BoZ6xdXFRYUoH1VwtC9iEQTHrLOUzI7DNniuTPKEZBvQOSTSBA==","signature_status":"signed_v1","signed_at":"2026-06-01T01:02:58.692222Z","signed_message":"canonical_sha256_bytes"},"source_id":"2605.30518","source_kind":"arxiv","source_version":1}}},"equivocations":[],"invalid_events":[],"applied_event_ids":["sha256:732065a66665a3fdb513f488bf20dc16a7e34896c006545ac7a0af2bde3c137e","sha256:3786e74bd102d980739dc51031e46f2676a7de47f4c5de4679c9b547778f7dc3"],"state_sha256":"fc484d0c9f35891fb5ae9cf7c58af473760a4aa911fc65bf428b19b108bda8f2"},"bundle_signature":{"signature_status":"signed_v1","algorithm":"ed25519","key_id":"pith-v1-2026-05","public_key_fingerprint":"8d4b5ee74e4693bcd1df2446408b0d54","signature_b64":"JA0ijkwY9ZraY+P8dEOdy/uQZZZ8T+Igpm4Iugtj7+NVUBtRFH6QPpm19uXgBn4W0IfvVpN7OOCYy/2qpOUfCw==","signed_message":"bundle_sha256_bytes","signed_at":"2026-07-03T03:31:24.753446Z","bundle_sha256":"17de6896f0208603688e08b473e2e2fc1aba09f36f69b07d8286008259fd688f"}}